The company TransMeta was mostly PhDs. They fooled around so long, arguing and redesigning, not releasing, that Intel ate their lunch steadily improving scalar performance. My colleague who was worth $100M in TransMeta options at one point, is back to work with nothing. So yeah, too many brains are a dangerous thing.
Consider also that a) most businesses fail b) many successful engineering companies were founded and/or staffed by professors, Ph.D. graduates, and Ph.D. students from Stanford and elsewhere, d) intel didn't do so great with VLIW (itanium) or low power/thermal (Atom lost to ARM - and intel seems to have squandered StrongARM/XSCale) either, e) intel probably had many more Ph.D.'s than Transmeta did, and they still hire tons of them.
Be that as it may, it's sad Transmeta died and its IP was sold to Intellectual Ventures, a company that has invented interesting things but also seems to make most of its money from lawsuits.