He's clarified his most outrageous remarks to a more reasonable position though. The problem is that you have social media people and tv media like comedy central or Samantha Bee who are constantly screaming racism and bigotry at every little thing. Just the other day Maher talked about how it was a mistake for him to cry wolf over how bad Romney and McCain would have been for this country, and then in the next sentence went on to state that Trump is going to be a malevolent dictator who will hold onto power at all costs. You're doing it again, Bill!
It also should be pointed out that a lot of these protesters are bused in and funded by moveon.org. The good news is that Americans don't like this kind of crap.