I think that in a lot of ways it's because of the roots of the organizations in question. Instead of saying "yeah, we have money, we can go buy this solution and trust in the vendor to support us" (an objectively viable solution in many situations) we instead say "we've got $100,000 in seed money and one engineer plus some friends she's convinced to help out pro bono, that won't buy us a sideways glance from Oracle".
Once you've survived the first year or two and gained some traction, suddenly the decision to investigate other solutions becomes a break from tradition -- and no engineer wants to throw away their work. It's incredibly hard to do a full stop, look around, and reevaluate your needs to see if you should just go in a different direction. I'm not sure I've ever seen it happen, really; we always just bow to the organic growth and inertia that we've established.
There is also a strong tradition of Not Invented Here (NIH) at work in this ecosystem. If it wasn't written by one of your peers (other startup people) then it's just not very cool. Use a Microsoft or Oracle product? Hahaha, no. Open source or bust!
To be fair, though, I've never worked for a startup that could afford that kind of software, so I guess the point is moot. I'm not spending 20% of my startup's cash reserves on software licenses to Oracle, when I can instead use that $2m to hire a few people to build it for me and know it inside and out. Plus, then they're invested in my company.
Also, please don't think I'm denigrating open source software with this commentary. I just think that the kind of zealotry that precludes even considering all of the options is, in general, a bad business decision, but one we seem to make all of the time.
Your expensive vendors sit on security patches for weeks and my free ones shoot them out almost immediately. Why is that not a business concern?
I don't think it's zelotry, there are a lot of advantages to open source software you aren't going to get from Microsoft. If you are an edge case and you happen to stumble on that race condition bug are you going to have your engineers black box test and reverse engineer someone elses product illegally while they wait around for Microsoft support or have them look under the hood, patch the bug and move on?
What the big licenses fees get you is accountability, which is of course a huge thing, but what open source gives you is control.
I think if your business is software, then open source makes perfect business sense, especially if one of your assets is a team of competent engineers.