The chronologically first verses about jihad revealed in Qur'an are (22:39-40) in those it can be seen that a call for war was allowed for Muslims based on an act of self defense and because of the justness of the cause!
As I wrote in my comment: This means the Muslims were only allowed to fight non believers when they have been suppressed and abused and in cases Muslims are allowed to attack to prevent the attack of their enemies, as they should also show power and let their enemies respect them or if necessary be afraid of them. One could say war in Islam is allowed for self defense and self preservation of a Muslim nation. This are the only reasons which go ahead with Islamic laws (shari'a).
Therefore we can read that Muslims disliked the fighting and killing as it is described in this Verse, but it was in cases necessary for saving their souls!
This doesn't mean that all Wars Muslims fought were from this kind.
Now in 1st place Muslims are more suppressed in their own countries! That's the main problem and because of the lack of a true leader and more or less self declared scholars with a bad half knowledge we see now what happens
I also found this additional statement made by @Shoaib as a part of the answer of the Question Does Islam have a concept of “innocent lives”?
"It is rather the "justness of the cause" that determines whether a life can be taken". Which applies in many of your quoted verses!
The Verses you have quoted
First most parts of these verses have nothing to do with war or fighting and if you read the bible or old testament you will find plenty of similar Verses speaking of God's (Allah's) punishment for sinners and non-believers etc and how believers killed or even massacred non-Believers. I'm not a scholar and I try to give a very short summary of what I read in different tafsir (Qur'an interpretation) books and I would recommend you to read different translations as you may get more information!
- (3:56) is related to the Jews who disbelieved Jesus or 'Isa (Peace be upon him) so one could say this verse is not even related to Muslims!
- (8:12) is related to the fighting/battle in Uhud, and is just a visual interpretation of the killing (Uhud was a battle that ended more or less badly for Muslims)
Surah 9 quotes a lot of rules of war!
Talking about rules I'd like to add: you should know that all battles Mulsims fought during the life of the Prophet Mohammad (Peace be upon him) have been governed as test cases for the Islamic jurisprudence, as they are either quoted in the Qur'an or a Hadith collection. But unfortunately one could conclude much of them, so it needs a true scholar to point out whether a case is applicable in each situation or not, of course this is fixed in books, but even those can be interpreted! Among this rules you will find that a fighting army shouldn't kill people who are not involved in the fighting like old people, children, women, preachers etc., this is one thing I really miss these days (even in the most modern wars like WWII, Vietnam, Iraq Invasion etc.)! An other thing is that in Islam as in all abrahamic religions suicide is a major sin!
- (9:5) shows that Muslims should stop fighting during a time period for example now we have the 5th of safar (2nd Month in the hijri Calendar) a month after muharam one of the 4 months where fighting is not allowed unless one needs to defend himself! Now an other issue about that verse is that there have been a treaty between Muslims and non-Muslims which was violated by the non-Muslims, and according this treaty declaring war was absolutely legal!
- (9:29) this verse again only make some rules, because after the non-believers have signed a treaty suddenly Jews tried to split this treaty etc. So the intention was to weaken them to create a kind of treaty with them.
- (9:73) Here the Verse speaks about the punishment of Allah for non-Believers and asks the Messenger of Allah (Peace be upon him) to fight (if necessary) the non-Believers, be harsh to the hypocrites, this Verse was revealed as Mohammad (Peace be upon him) treated them or used to treat them before that very kindly, but as it seems this was no more useful Allah ordered him to change his behavior towards them!
- (17:16) Is only a description on how it goes that a town was punished by Allah, again this is not related to Muslims themselves: see the translation of Muhsin Khan here.
A bit off-topic, but a try to understand the violence
Of course some of these verses you mentioned my lead some miss-leaded Muslims to fight and kill without respecting any of the rules of the shari'a! Not only because they misunderstood them, but mostly because they have such a hate inside them and seek a hint of a proof to justify the vengeance they want to take, for many reasons like:
- actually Muslims and Muslim countries are weak,
- most Muslim countries are not democratic by any means and people living there are mostly suppressed,
- especially scholars of the wahhabi/salafi school indoctrinate that Muslims are not allowed to revolt against a Muslim leader if he acts like a Muslim (praying etc.)!!!
- they dream or glorify the past and would like to have a caliphate like in the early days of Islam,
- they use these Verses and other narrations to justify their conduct (maybe more for themselves and those who feel the same and sympathize with them)
- in the Muslim countries the rate unemployment of young people is very high so some of them seek help or refuge in religion, and fall into the arms of scholars with radical thoughts!
- by being part of something new (creating a caliphate etc.) they feel being beneficial which is totally different from the feeling they had when being jobless!
- Muslims are disappointed of many other countries like USA, GB, France etc. because they support the dictators ruling in their countries.
- there are many other reasons I couldn't count which may more or less have influence!
- Muslims are always thought and recalled about the "glorious days" and when they look at their present situation they would like to change it.
- Muslims in many Muslim countries tend to see incidents from a point of view Muslim vs. non-Muslim, which creates a hate towards non-Muslims or a feeling of injustice: For example Israel vs. Palestine, actually the attack in Paris vs. thousands or more Muslims killed each day in Iraq, Syria, Israel etc.
One important point is even if the amount of radical Muslims would be low there are many Muslims who sympathize with them for many reasons which can be more or less the same as above!
On the other hand I would like to say that you missed a lot of Verses and narrations from hadith collections (see for example this sahih hadith) which I would primary regard as a basis for this violence (If taken literally and out of their context).
Does it follow then that the non-violent Muslims simply just do not feel "suppressed and abused" at this time and therefore remain non-violent, but if in the future they do feel so then the Koran can justify violence toward non-believers?
Well as I mentioned the biggest suppression comes from the governments or regimes ruling in Muslim countries, so non-violent Muslims do their best to live their lives as good as they can, but those who can't hold the stress (might) end up as what you called "violent Muslims" or leave their countries (and even among those some get indoctrinated by the wide spread wahhabi sympathizers). So the point is that you can only make an end of this stress by a change in those countries, some regimes already made small steps towards what one could call democracy. And I think non-violent Muslims could refer to the following (linked) Verse.
And Allah knows best!