You are absolutely right. You should only make supplication against enemies who are fighting against you.
Source: Saudi Islamic Affairs
You can see that many scholars would make supplication against the Jews, this is totally wrong and shouldn't be done. This all stems from the Palestinian/Israeli issue.
Many people will generalize that all Jews = Israel and all of Israel = Jews, which is totally incorrect. You can make supplications against those who attack and kill Muslims, but do not generalize, which is I think what is happening here. This is similar to many Americans who say "Muslims are terrorists", yes there are some Muslims who are terrorists but compared to the Majority its a small amount. Muslims and some scholars are doing the same against the Jews.
We can also learn from the prophet PBUH when he went to Alaqaba to make Dawa to them and they ordered their children to throw rocks at the prophet as he was walking out. Allah gave him the option to destroy them but he instead asked for forgiveness incase some of their children might become Muslims and help the Muslim nation out.
As Muslims we should always be making Supplication to guide people to the straight path, not kill them.