should we judge a whole religion by the acts of some in that religion ?

Way to answer your own question, buddy.

It depends if those acts are doctrines of that religion. For Jones it wasn't. For the 911 Muslims it depends. For the atheism of Hitler (and he certainly was an atheist because of the value he placed on Nietzsche) it does fit with the doctrines of that belief.

No, that is blanket demonizing

Jim Jones actually became an admitted atheist but saw religious emoting as useful manipulation for control

Hitler hated orthodox forms of Christianity , especially Catholicism which he nominally belonged to, as " Jewish disease" that weakened the German Volk

All the Muslims I know reject Jihadist islamism and all the use/misuse of Islam to promote terrorism

No,many horrendous things have occurred in history by deranged individuals claiming it was in the name of God,only fools and atheists would believe it.

every religion has there naughty past. There would be way more religious persecution if we judged everyone based on religion.

And those people who don't believe in any religion they are even worse.

Let's not.