Science included? I think so.
Science has a method for improving what it's right about, and finding what it's wrong about. I see no reason to take the opinions about reality of anything that doesn't have such a method seriously.
Stile, my problems with atheism, and or atheists, is that they pretend to not believe in something, for one.
What does not believing in something really entail? For my part, it's really not that I don't believe in god(s), it's just that I believe in something that doesn't leave room for them.
2. they say they won't subscribe to a god because of lack of evidence, when the bible clearly states that it is by faith that you get to know God.
Yeah, that particular piece is a sizeable part of the reason I find the Christian notion of God so unacceptable. No, I will not have faith. Faith is a cop-out, it is a shoddy alternative to knowledge, it is what you have when you don't know something. Parading it around as a grand virtue is obscene*.
3. they say they don't have a problem with people having faith (so long as they are not doing harm to anyone) then go on to compare faith in god to santa claus, or the easter bunny. You are not respecting people when you do that, you are insulting them.
Outside of arguments about religion I tend to extend every respect to other people's beliefs. But if you're going to get into an argument about it, then, yeah, I don't see the difference. I don't think theism is an philosophical idea inherently deserving of my respect, I think that robbed of its history, no-one would take the idea any more seriously than we take the Easter Bunny.
4. they resort to history books and point out all the bad things that were done in the name of god/s
The problem with religious history is not that bad things have been done in the name of God, it's that there's no sign of those who believe one thing or the other behaving any better than anyone else (with the exception of the Quakers who, frankly, rock on toast; seriously, has there ever been a group of people with such a consistent history of being on the right side of moral arguments?).