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sketerpot comments on A puzzle concerning CS major vs. engineering major salaries - Less Wrong
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Silicon Valley lore is that top programmers are 10x as productive as regular programmers (see Joel Spolsky or Paul Graham). I once attended a lecture series where entrepreneurs from Silicon Valley came to talk, and one point they kept hammering on was the importance of hiring the best people. So if coming from a top school makes SV employers think (correctly or incorrectly) that you're a top programmer, this could go a way towards explaining the salary thing.
This also works if coming from a top school correlates with some factor that makes SV employers think you're a top programmer. The most obvious example of such a factor is programming skill: you'd expect people at top schools to program better, on average, than people from obscure schools.