Often, people look for persecution to make themselves feel superior or to sell a story in the Washington Post. Many times, the deaf in America loved to compare themselves to the African Americans of a time when prejudice was so out-in-the-open that they had to drink from different water fountains. The problem is that, while some prejudice exists, it is offensive to the African American to try to make such a claim. A deaf person can walk down the street or into a room and is not automatically identified like a black person is. Same with atheists and homosexuals, sometimes the same with Jews.
Such prejudice existed and exists against homosexuals, the deaf, and atheists, but it is really completely different. I definitely wouldn't say that most Americans don't like them. To say "lots of Americans just don't like them" really isn't clarifying enough. If they mean that there are still lots of ignorant Americans who hate anyone who doesn't worship like them and condemn the things they condemn, sure. Those same Americans who dislike atheists probably still hate homosexuals and Jews and many of the white ones probably hate the black ones (and visa versa).
The Boy Scout thing is a good point, but how many young boys declare themselves as "atheists" ? It does hurt them when their parent tries to use them as a tool to drive this point home. I would let my son join and just help him see through any bunk about God that the Boy Scouts pushes, although I doubt they spend much time pushing much religion at all. I would need to see data on the military thing as I think it is based on old information that isn't used anymore.
Atheists are not denied "the right" to assume office, nobody has "the right." They do lose the vote because of ignorance, but that doesn't equate to hate, just ignorance. If the media wouldn't push so hard for any issue whatsoever, I imagine the fact of a political candidate's atheism would not prevent him from winning in many places. But the media will always point out that a candidate is a Mormon, a Jew, a Muslim, or an Atheist because it's so different. (I would not vote for the Mormon as they are cult members, but I digress.)
Many of the statistics in the article might be helpful, but spin is so easy and deceptive in these areas. Many, if not most of the stats here might have different factors that really affect them more than belief vs. nonbelief. I very much agree with this: "So when the likes of Glenn Beck, Sarah Palin, Bill O’Reilly and Newt Gingrich engage in the politics of division and destruction by maligning atheists, they do so in disregard of reality."
This one suggests there is something wrong with the suggestion that Americans dislike atheists: "Despite the bigotry, the number of American nontheists has tripled as a proportion of the general population since the 1960s."
Perhaps, the real point is that old-school thoughts are dying out and younger people are learning more without religion and are relying on science and mankind to solve the problems of mankind.