Because Christians think that America is a Christian nation or at the very least want to turn American into a Christian theocracy.

To be fair, it's not all Christians; some may disagree with something religiously or morally but can still see its legal validity.

However, here are a few common reasons, though it applies to anyone, not just atheists:

1. Obviously, the biggest one is that some of the things that are legal or being considered are against biblical teachings. However, you have to remember that God said not to kill, and that's law, so why not other things He commands? That's where that's coming from. Of course, there's one obvious argument against this, which leads us to #2.

2. A common argument from anyone trying to make America "secular" is "Our founding fathers never intended this to be a Christian nation," or "Our laws aren't biblically based," or other variations. While some arguments for a "secular" nation are well-founded, this one is downright asinine. The pledge mentions God. Our motto is "In God We Trust." They made the decision to take the presidential oath on the Bible. They frequently reference God in addresses, speeches, letters, and documents. Ben Franklin called us a "Christian nation." The basic laws and framework for the Constitution are based on Christian values, and while it can be argued that some of those values are shared by other religions, the Founding Fathers weren't made up of all kinds of different religions. Even those who were Masons acknowledged God, as did the (arguably) agnostics of the day.
I personally get agitated by this argument not because of the subject matter, but because I get agitated by any baseless argument made by someone who can't bother to read a book.

3. While some separation of church and state may be okay, or even necessary, there is a kernel of fear that it will be taken too far. You have to remember that to Christians, God is the source of morality. Therefore, the further you separate from God, the further your morals become compromised. There is a fear of watching the country you love, your home, slipping into moral decay.
"Morals," remember, are not "values." What is or is not valued varies from person to person or culture to culture.

Anyway, as for the mass majority of Christians who get riled by the thought of "secular" America, those are a few common reasons. This, of course, does not include extremists who likely have a whole other list of grievances, such as those out of Westboro that even Christians don't like too much.