I imagine that the relatively low number of tweets is in part due to the fact that most tweets don't include hate speech.
It's interesting to see that when you zoom in on the map you find, like the article says, that there are not large concentrations of these tweets from large cities like New York City, Boston, and so on, but from relatively lower population areas. If it were a matter of population alone you would expect the cities to have brighter blobs on the map than they do. That alone, I think, is something interesting to take away.
And personally, I think that a person who says "retarded," "gay," and similar words even without specifically taking about LGBT people or people with disabilities are using hate speech. Intent isn't the only part of it. There's also the effect your language use has regardless of your intent. If I said "I don't mind people of other races, whether they're negros or Chinamen" I'd be sending a mixed message to say the least.