1. Startups have a high(er) chance of failure or pivoting into something you didn't buy. ("Fail fast" is a popular mantra [a])
2. If the startup does have an "all-star team" as you say, they're more likely to get acqui-hired by Google/Facebook and the product subsequently shut-down. (I've said before that this is a byproduct of the acqui-hire craze and I still believe it).
3. Many startups (especially those with all tech founders) seem to suck at customer service. They tend to focus on automation and hacking their way to avoiding any type of high-touch service (the exception seems to be companies that make support tools). Do you prefer phone support from your software vendors? Don't choose a startup.
4. Their pricing doesn't fit your buying model. Many government and educational institutions must buy using a PO process. Large companies don't want the "small team plan" for $29/month.
FYI I'm not posting this comment to be a prick–rather it's a thought exercise. If you want companies to purchase from startups more often, stop trying to convince them why they should and start addressing the reasons why they don't.
[a] http://www.feld.com/wp/archives/2009/04/the-best-entrepreneu...