It can be a double edged sword, no doubt about it. But I've often found that it was the "Trek Haters", for lack of a better term who drew the first blood. Many younger fans either don't know, or more likely don't remember the late 60's and early 70's, when Star Trek fans were considered weird in the extreme, not just by their peers, but by William Shatner himself. For some reason that has never been explained, people just look down on Star Trek fans.
I don't think there were "Trek Haters" in the way you mean it, and especially not at that time. There were bullies, intent on a game of power and aggression, preying on the timid, the nerdy, the loner, the daydreamer, types that for one reason or another tended to gravitate towards Star Trek and other stories. So, within a short time, Star Trek became a fast way to identify their preys, and the stereotype only grow from that.
As for Shatner and others, they weren't probably prepared to the obsessiveness of some fans, wrongly labelling the entire fandom due to these few people. Also, you shouldn't draw too much from one SNL sketch.