I don't think I explained my point of view on that particularly well. What I meant was MySQL is backed by a single commercial interest (and as of this year, that commercial interest is a Big Corp). Somehow, someone has to make some money pretty directly off MySQL, and that someone has a lot of influence on the direction of MySQL. Much more than, say, IBM could ever have over the Linux kernel, despite the fact that they put money into it.
To me, that's a conflict of interest. Plus it creates uncertainty about what might happen in the future. Sun's already talking about closing the source of some of the tools (I doubt they will ever close MySQL completely, but still...). If there's a choice, I'll usually go for the OSS project that is not primarily controlled by a company. e.g. Perl over PHP, Debian over Red Hat.