Top 10? Top 20? Because I did a quick count a while back and found at least six of the top ten used MySQL in some capacity. And two of the remaining four were owned by Microsoft. :) I'm no DBA, but that suggests to me that MySQL is pretty suitable for large websites, compared to the competition.
I don't think anyone is saying that MySQL is not suitable for large websites. However, the reasons why top websites (and non-top websites) are using a particular piece of technology is usually far more complex an answer than "best technology" or even "good technology". Exhibit A: IIS.
So I'm curious about this, actually. You'd think sites like Google and Yahoo! would be smart enough and have enough resources to use the best tools available.
They do. Google ditched all existing database and built their own system to handle their main stock and trade. For some things, they use MySQL, albeit a modified one.
Yahoo uses PostgreSQL (again, a heavily modified one):
http://www.informationweek.co/news/showArticle.jhtml?articleID=207801579
Keep in mind if popularity alone was a good criteria, we'd all be <strike>happily</strike> using Windows on our desktops. If all that mattered was technical superiority, we'd be running BeOS. :)
Frankly, the choice of using PHP as the language for MediaWiki has probably caused more problems over the years than the choice of database backend. :)