Brennan (Bones) appears somewhat cold & Greg House of course is as you stated an arsehole. These characters play into the stereotype of the "typical atheist." Don't get me wrong though I actually like both shows & love House as a character.
Unfortunately when a character is an atheist or agnostic in a movie/TV show they usually are the bad guy or are jerks. If not a jerk then they get it wrong, screw up or something. Atheist are almost always shown in a negative light.