I was sitting in the audience as they got into the part where Bottom acts like an ass and this is supposed to be funny. I was just waiting for them to get it over with, and then remembered that there was nothing after it in the play that I looked forward to anyway.

Your unease may be from the audience reaction, not the action on stage. The action on stage is black magic, in which the King of the Fairies can get away with it because he is powerful enough to escape the consequences of black magic dabbling. This is pretty damn terrifying and not funny at all if you think about it. We are all there in the audience watching a comedy and we don't want to be terrified, and we don't want to think too much. But why do people laugh at that on repeat viewings? I'll try and make a mental note to check if I laugh the next time I see it; that would be a rude surprise.

What thou seest when thou dost wake

Do it for thy true love take

. . .

Wake when some vile thing is near

adds up to one of the worst curses in the library. Shakespeare violated the prime directive of karma with this plot element and he got away with it. Who's to say whether that is the greatest genius but it certainly is skill.