I feel all the hate towards Elven kind is primarily directed towards the Thalmor. Since the Thalmor are Elven supremacists and highly favor elves, people assume that ALL elves associate themselves with them. Since the Thalmor are viewed unfavorably, many come to hate elves.
P.S Nothing wrong with liking the Thalmor either...I do. Even though they are morally corrupt in their tactics.
Were the Ayleids Thalmor?
In a sense, yes they were. They did see themselves as being the superior race in Tamriel, perhaps justifiably, as the Thalmor do. They also employed ruthless and efficient tactics to exert this belief, much like the Thalmor. As for me liking the Thalmor, it would only hurt my image in the eyes of those who's views are opposite to mine. The Thalmor means something different to different people: some see them as cruel fascists, others as the righteous rulers of Tamriel. It all depends on how you look at it.