seems a little cherrypicked, doesn't it?
Atheists not allowed to live? Sure, somewhere in the universe you can find a place where they might kill you over it, but you could find a place where they'd kill you over anything.
Atheists not allowed to form a club? Several universities have "atheists clubs." I know this for sure. You could find some universities that won't have an atheists' club, but you can also find a university that won't allow a White Students' Club, and some that won't let the military recruit on campus, etc.
Not become a boy scout? That's like saying that an atheist is not allowed to become Pope. Of course an atheist won't be elected Pope, because the job description says you have to be the spiritual and political leader for a particular religion that is monotheistic. Similarly, the some Boy Scout troops partner with religious denominations. There are Boy Scout troops that would welcome atheists, of course.
An atheist can't run for office? Balderdash. Many atheists have run for office, some have even been successful. California has had an atheist governor and there have been several atheist congressmen in the past. If there are no atheists in congress currently, it is because they have not been elected by the people. This is not to say that they cannot run for office.
There is some prejudice against atheists, just as there is some prejudice against Mormons, against Jews, against Muslims, against Catholics, etc., but this article is over-reaching. I didn't read the other one.