Again, it does and it doesn't. Most superheroes hook up with women who are essentially lesser than themselves. Lois can't identify with Superman's past. Bruce Wayne can't hold onto a woman for this very reason*-he can't relate to them. But while MJ may not have the SAME pains and dramas in her life, (you're not gonna find too many girls who indirectly caused the death of the person who meant the most to them) she does have her own demons and as we found out later on, she too, hides behind a mask. This makes her able to understand what Peter goes through. And she has been the best support system through it all. Venom, the return of his parents, the discovery that they were fakes, the unmasking-I think most women would bail on you the second you find out that you're a clone and smack the hell out of them. Mary Jane has been tested by fire and she has stood with him through it all.
(*among others, obviously.)