A lot of fans have always held a grudge against him for the anti-slasher crusade, and for trashing THE BEYOND when it was given a theatrical re-release in the late 90's. In fairness to him though, he only watched it once, and THE BEYOND has many admirers who nonetheless admit that it took them multiple viewings to warm up to it. Also, asking a thoroughly mainstream critic of his generation to appreciate Fulci was probably too much to hope for anyways.
When you exclude horror films from the equation, I have found that Ebert's taste in movies is very similar to my own. I have also found that when I agreed with an Ebert opinion I usually really agreed with it, and when I disagreed with one of his opinions I really disagreed with it.