There's nothing wrong with discrimination in and of itself. It's actually desirable in a lot of cases. For instance, discriminating based upon competency/intelligence is a good thing. Discrimination only becomes a problem when you're discriminating based upon an |irrelevant| characteristic. (Relevancy is determined by your priorities and/or values.)
"Is it their fault that they're less intelligent?"
Nope, it's not. But that's not the issue. A lot of people think society condemns racial discrimination because race is an attribute outside one's control. That's part of it but not the full story. The real reason it's maligned is because, all other things being equal, race should have nothing to do with an individual's competency or worth as a person. The fact that someone has no influence over their own racial makeup just adds insult to injury when they're judged by it.
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I've often wondered the same thing you mentioned about intelligence. Everybody is born with their potential; how can you laugh at a part of somebody that they can't control? But life would be rather joyless if you couldn't occasionally celebrate favorable comparisons between yourself and the rest of the world. :)