I would absolutely say that Dawkins was in fact "going after him" and being an asshole, even if he probably didn't fully understand why (but that makes the whole situation even sadder, that a scientist so visible to the public would be clueless about how to engage kids about science and engineering).
Don't forget that Dawkins said that Islamophobia is a 'non-word'[0].
Dawkins was being an asshole, and he definitely knew why. Ignoring Ahmed Mohamed's religion and race and pretending like it's not relevant doesn't change the fact that this entire incident is inextricably linked to the fact that he is Muslim and not white.
[0] http://www.independent.co.uk/news/people/richard-dawkins-def...
Based on what proof?
There are various forms of malice and incompetence that can explain the official acts at the basis of the incident, so while there is certainly plenty of reason to think that might be a significant factor, I think its far from clear that it is.
The responses to the incident from various circles certainly provide plenty of evidence of both racism and Islamophobia, but I don't think its fair to say that it is unambiguously the case that the whole incident boils down to that (though I don't think its particularly unlikely.)
It's a valid design/art form.
AFAIK, all Dawkins said was that he didn't build a clock. Which he didn't, he took a circa 1980s Radio Shack clock out of its case and mounted it in a pencil box.
Apparently trivially verifiable facts are discriminatory now?
This whole thing stinks. I've seen nothing in either the police reports, the words of the involved people, or any hard, objective facts that indicate that this is a matter of anything other than garden variety school administrative stupidity.