There is a fine line with an overtly "atheist" character (i.e. they talk about it all the time).
It can be done well as with the following:
House
Bones
Sheldon Cooper
Lisa simpson (earlier on in the show, I think she's buddhist now)
Star trek TNG Characters(minus races that have religion ie Worf)
The Doctor from Doctor Who
Stargate cast
But if the entire point of the show is having a character talk about atheism and how smart that makes them you end up with a person just as annoying as an overtly religious character. it really isn't neccesary IMHO. This can be seen very well in the show Family Guy, as the character of brian the dog has gone from the "staright guy" character to a bleeding heart soapbox hippie asshole who won't shut up about his own opinions. this makes him by far the most unlikebale character I've seen on TV, and would make me punch him if he was a real person. I'm not sure if the people who wright the show want you to like him or hate him honestly. I would rather hang out with a racist tool like Archie Bunker than Brian Griffen, because at least Archie grew in the show as it went on.
