The difference between Christianity and Islam is that muslim is a false religion. Disagreeing with a false religion does not equate to hating those who practice it.
Atheists tell us that all religion is false.
That tends to be the case I think, though perhaps some variants of atheism wouldn't put in that way. And those who do see them as false religions don't necessarily hate those who practice those religions, though there may be a lack of understanding and appreciation.
But using political power and harassment and fear against those you disagree with, that is hatred.
