First, it is really dangerous of normal Muslims (i.e. not scholars) to conclude fatwa or hokm (Fiqh ruling) directly from Quran and Hadith by themselves without the proper Islamic knowledge.
For example, if someone read this Hadith and concluded from the verb in order that it is must for a person to pray in shoe it will be truly wrong conclusion.
The order in this Hadith is Sunnah/Mandoob not a wajib and scholar says it is left to the current practice. So in short, if you are in a Masjid with carpets and people take off their shoes you should take off your shoes as well.
On the other hand, if you are in a place that you walk normally by shoes (i.e. outdoors or park) and you wanted to pray it is better to pray in shoes.
The claim that you should not do this because of the chance that the shoes can be impure is false, especially in modern cities. Because even if you stepped over something impure and walked after this it will be cleaned by the walking after.
If you see something attached to your shoes that you are sure to be impure, just scratch it away and pray in them or you can take them off (which is literally very hard to have these days in modern cities)