Dear Ms. Snark:
I really love your blog, thank you so much for sharing, (and venting).
My manuscript is complete and polished, my query is professional and enticing, and I have only queried agents who are actively looking for manuscripts in my genre, (commercial fiction). However, my subject matter is controversial.
How do I get an agent to look past the fact that my story involves abortion, and see that the overall story is worth reading. I will greatly appreciate any suggestions you can offer.
Well you've heard it here often enough: write well, but in this case you're going to meet the other reality of publishing: every agent has topics they won't read. This is one of them. Child abuse, sex abuse, alcohol/addiction recovery stories are some others.
Particularly with abortion, it's very very hard to get past "this is an important message from our author". I hate message books.
It's also very hard to be funny about abortion. No, it's impossible. Not even mordant, dark humor. And humor can be illuminating and carry a message much more effectively than any kind of "serious exploration". I don't look for serious explorations in commercial fiction. I run and hide from them in fact.
So, short answer: you can't.