A major foundation of our country is protecting the rights of minorities- you can use that same argument to justify racism- there are more whites than blacks- so why should I have to serve blacks in my restaurant if I don't want to?
Companies training employees to say "Happy Holidays" instead of "Merry Christmas" is strictly a business decision- government has nothing to do with it. And if it bothers you you are free to patronize a store that doesn't- but atheists have no choice about public buildings like city hall or the courthouse.
No child is forbidden to say a private prayer in school or even have a Bible to read in their free time. But it's not the school's job to do this. If you want religion taught to your kids- you can do that at home, in churches or in a private religious school- nobody is stopping that.
And considering how many priests have molested children I don't think you can say religion prevents crime.