1. Sense of Entitlement - Some MBAs have a sense of entitlement about how much responsibility and status they should get. When joining a large organization, there is some (limited) basis for truth in that high self-regard. But in a startup context, this is laughable. This also translates to salary expectations, as John points out:
Top MBA programs are expensive and their graduates have astronomical salary expectations.
3. VCs - Some startups resent VCs for all the obvious reasons. Many top VCs are MBAs. Therefore, startups resent MBAs. It's not just that they possess the degree, but also that many of them are a different "breed": the business-type. As a result of this negative sentiment, look for VCs loudly -- and sometimes inauthentically --proclaiming themselves as geeks, entrepreneurs and CS majors (even if they can't write a line of code anymore).
4. Lack of Product Orientation - Startups have to be product and engineering oriented at the outset. Many MBAs don't have technology backgrounds and are making a career switch, and are therefore not a good fit.
5. Risk-Aversion / Un-Contrarian-ness - Startup people are a bit crazy, believing something many sensible people don't. Some MBAs are perceived to be conventional thinkers, and come from a background of high and steady achievement, without huge spikes with creativity and risk-taking. Stanford MBAs, for example, are diverse in many incredible ways, but not so much in undergraduate academic institutions - almost 1/3 of my class came from Stanford, Harvard, Princeton, Yale and Dartmouth (of course, founders of Facebook, Quora and many other sites also came from those same schools).
Needless to say, none of this is to say hatred or prejudice against MBAs is justified. Indeed, many of Silicon Valley's most highly respected entrepreneurs are MBAs, such as Scott Cook of Intuit and Vinod Khosla of Sun Microsystems. But that is a topic for another blog post.