Hard to believe the whole mess was three long years ago. But, here's a video about it that I think glosses over some important details:
I think it was fine for Watson to suggest that men ought to be conscientious of their surroundings when asking a woman out. It's important to note that Elevator Guy did not say anything rude or overtly sexual, nor did he touch her or refuse to take "no" for an answer – he just left. Nonetheless, there's a chance that he could have turned out to be Creepy Molester Guy and he ought to have been aware of how his surroundings might make a woman feel.
Where Watson tripped up was when she said, "it creeps me out when guys sexualize me like that". Let's revisit this: she was asked out for coffee after a trip to the bar. By that logic, any time a man ever asks out a woman, no matter how innocuously, he is "sexualizing" her. I'm not sure what else she could mean by "sexualize", since the rejected fellow just quietly left after she declined his invitation. She never accused him of touching her inappropriately or saying anything vulgar or suggestive.
Sure, the vulgar and threatening comments are uncalled for, but it's not as though Youtube comments are representative of the skeptical community as a whole, or the discourse that occurs at conferences. Besides, there's an old saying on the internet: don't feed the trolls. When Watson gets upset about the trolls' comments, she's just giving them the undeserved attention they're after.
My feelings on the whole issue were summed up in a comment on the above video, which I'll paraphrase: Some have called Rebecca Watson a professional victim. I only know that three years later, she's still retelling the horrible story about the time she was asked out for coffee after a trip to the bar.