1. Plenty of heroic art has ambiguous villains, but this is certainly a modern preference. I'm sure our view of Hector in the Iliad being sympathetic is quite different than the ancient Greek's take on him.
2. The racism issue is quite real, in my opinion. This problem is somewhat exacerbated by the movies, where all the orcs have dreadlocks. But to say the dark races are "mislead" just substitutes stupidity for malice. All the heroes, without fail, are white. The elves, clearly the highest race in Tolkien's world, are white, blonde, tall and beautiful.
3. 3 women, all of whom have bit parts, at best, isn't really that great. Though they are all shown to have great redeeming qualities, two of their characters mostly revolve around their relationships with men (both of whom are in love with Aragorn, a great virtue, it seems). Galadriel is the only one who seems to have an identity and power that does not rely on her relationship to a man. Though even she appears to be secondary to Celeborn when she again appears.
This is not to dismiss LotR as not good or important literature. All these criticisms could be made of the vast majority of western literature up to the late 20th Century. The Iliad has no female or low class characters at all (the Odyssey's introduction of Penelope, Eumaeus and Dido is really a watershed in western literature, and their characters are far weaker than anything in LotR), but is still studied. Because of this, I don't understand Tolkien apologism.