Fenris hates every Mage Everywhere because one population of free Mages in one country misuse their power. If his anger where concentrated on Blood Mages then I would be more sympathetic but he desires EVERY Mage to be treated no better than he was just for being born as they are.
But that one country is his sole experience of what mages can do. He isn't advocating slavery (because as crap as it may be, the Circle isn't slavery) or death, but control because he's had first hand experience of what can happen when mages are completely free.
That was entirly his choice. He was openly hostile to both Anders and Merrill from the begining. If he had set aside his prejudices he could have found some common ground in that he and Anders both dislike Blood Magic and a common history as an Elf with Merrill.
Right from the beginning, Anders treats him as less than human - why should he be the one to put things (which come from a lifetime of abuse) aside, when no one expects Anders to do the same thing?
He doesn't have much of a common history with Merril, not really. He even says this, that it's not his history. Most of his identity is tied to his past as a slave, not so much as an elf. Any cultural ties he may have had would have been lost anyway, post ritual. And I'm not really sure why he should be obligated to, either. Because they're both elves? The blood magic issue is a fairly big block, and he thinks she has thrown everything away for something that is useless.
Don't get me wrong, I like Fenris and his treatment at the hands of the Magisters was inexcusable. I understand his feelings towards Tevinter and even Blood Mages in general but his hatred of Mages everywhere who have done nothing to him is unwarranted
See, I see those two things as somewhat contradictory. His only experience with free mages *is* Tevinter. It might be an extreme example, or a not going to happen anywhere else example, but it's the only one he knows. Every mage he meets will get compared to that until he can trust otherwise, which is a not completely unrealistic stance (it might not be nice, or fair but I do think it's an understandable reaction). Especially given how long it takes him to trust and make friends with others.
There are a good number of Mages we meet, and play, that are contrary to Fenris' views ...
I was referring mostly to DA2 and the ones that he would have interacted with (Fenris meeting Wynne would have been interesting, though and i do wish there was more direct overlap). And for almost every one, you can counter with someone who does pretty nasty ****. Like Quentin. And Orsino, who is doing pretty much what Meredith accuses him of.
I generally don't count the player character, since you be a spectacularly not nice person, but not get called out for it (ah, resources).
I would argue than many of the Blood Mages we meet throughout the games were pushed down that road by the Templars. It was not their goal to enslave others but to survive. I see them as no different than Fenris who freely admitted that he too slaughtered his way to freedom.
A lot of them are. Those ones (I think Trask's daughter could be used an example) aren't really any different, in that they've done bad things to stay free. There's also plenty who do it for less noble reasons, and it's not completely unwarranted to be afraid of those and since any mage can turn to blood magic, you have no way of knowing which ones aren't going to use it against you.
Like I said, I think it's sad that he gets very little fan empathy, especially give his fairly horrific back story (other reasons aside, people don't seem to look beyond EW BAD MAGES, without really looking deeper. Do most people play mages, and therefore take it personally? mostly for funs, retorical question), and I think his romance adds a lot to understanding him better.
P.S. I was serious about my first question. Why is Fenris the only DAII character with a theme song?
Because he's just that damn awesome 
Is it hate or really fear? I don't think it is anger so much as I think it is fear. Is he really different from person who would kill a spider because it was a spider? If we asked do you think that person really hated that spider or killed it because it is something they fear?
Definitely fear (tho really a bit of both). One of the first things that hit me was how similar his reactions are to fear aggression in animals (particularly dogs and horses, but that's primarily where my experience is). It's also not dissimilar to PTSD, which I think is totally relevant (and has been pointed out before)