So why condemn those who choose to follow a belief system that atheists do not understand?

It's the belief system that gets condemned, not those who believe in it. We leave the believers to do the condemning, then we condemn them for their condemnation, not their beliefs, which are are wholly & utterly irrelevant to the misery they espouse. I condemn you for your homophobia, not whatever bollocks you might use to justify it - though I condemn that too of course, but on a more philosophical level.

Atheists are atheist not because they don't understand the belief systems, rather because they understand them too well, i.e. in the objective sense of seeing them as Belief Systems in the first place, rather than as being literal truths. Part of Human Evolution is the process of coming to knowing both Ourselves and the Cosmos of which we are eternally a part. In the face of such Knowledge, mere Belief falls away into the same realms of cultural archaeology as superstition, mythology and folklore.