Dude... you're the one who said you were puzzled.
The bottom line is that when codifying the rules that we all have to live by, ALL people with a religious law book in their back pocket MUST have a reason other than "God says..." or "My religious story book says..." before restricting the behavior of all.
If you can't accept the lifestyles of the people who don't share your beliefs, you had better have something in your reasoning other than your ancient stories for why a particular activity should be punished or a particular life-style given second class status in the Civil Code.
This is all that the tolerant atheist asks.
Are there plenty of examples of intolerant atheists?

Is The Pope a Catholic? Generalizing should of course be avoided.
So that should be construed as intolerance? Why are you assigning these things to me?
Your opinion of Christians is stereotypical, and honestly, you are too lazy to find out the truth of my faith. You would much rather sit back and judge it from an ivory tower aloft. It's rather disappointing. Avail yourself of knowledge before you dole out your judgements.
If you can't accept the lifestyles of the people who don't share your beliefs, you had better have something in your reasoning other than your ancient stories for why a particular activity should be punished or a particular life-style given second class status in the Civil Code.
Um. I do. I am a firm believer of the law as well. Just because I am a Christian does not excuse me from obeying the law. The Bible says love one another, love thine enemy, do unto others as you would have them do to you, etc.
There are plenty of things that suggest we don't treat other lifestyles as "second class." In Romans 13, I am commanded to respect the governing authorities, thusly the law, because just law is divinely inspired. Thus if I disobey the law, I disobey God.
I don't know where you're getting your stuff from, but it is intellectually dishonest. I don't have to accept any lifestyle, nor do you. But you sit there demanding I accept yours. In this land of freedom, that's too bad, my friend.
And as far as generalizing goes, you administered a heavy dose of it earlier (and I'm paraphrasing here), "If this is how Christians act, then I want no part of it. This is why they get no respect from me."
Lastly, who do I want to punish? What are you afraid of?