As a Christian, I love my friends, regardless of their faith. It's following Jesus' example.
Would I stop being friends w/ someone because I found out they were an atheist? I haven't so far, and probably wouldn't.
For me, this question is a bit tricker than it first appeared. I have a number of friends that are atheists, and that has not had any significantly had any effect on the quality of our friendship.
I do, however, have a couple of friends who belong to what seems to be a subset of atheism. From experience, there seems to be a small group of atheists who aren't content to just believe what they believe, but also find it appropriate / necessary to sneer at people who don't believe the same thing that they do.
These folks are my friends, but when they're rude to my faith, it feels disrespectful to me. I've talked to them about this, so its not like they don't know.
Some of them backed off. Some didn't.
And, if an atheist "friend" continued to be deliberately rude to my faith, when he knows that its hurtful, that could eventually end that friendship.
The atheism would be a contributing factor, but not the cause. The cause would be disrespect...