Not everyone hates Stryker, and in fact the majority like him or don't care either way. The people that are constantly lashing out and spewing hate on him, are the ones who are negative to begin with, and just love to latch on to something, and refuse to actually give it a chance. There's many characters in MK post MK1-3, that I don't care for, but there's none I care enough about to actually hate them. Takes a lot more energy to hate, than it does to not care for something. In the end, it's just a character in a fictional game, not really anything to get all worked up over if you ask me. I tend to enjoy things much more than I hate or dislike them, and everything is so much better that way. Couldn't imagine a life filled with such negativity, that a video game character is something to stress over.
I think it also has to do with the fact that a huge bandwagon went around where people just hated on the character, just because it seemed like the popular thing to do. I never bought into it, and I'd say he's better than all characters who debuted in MK4-MK:A, save for maybe a few characters like Quan Chi or Kenshi etc.
As for my own personal opinion, I have never really cared one way about Stryker. I've never hated or liked him, he was just there. He is fun to play as though, and I do not think he doesn't fit in the game. He's a human character who relies on his gadgets and weapons rather than super powers, does that mean Batman and Iron Man aren't fit for the super hero universe as well? He's different, there's nothing wrong with that.