Erm .. making money wasn't specifically what concerns me.
Many (many) moons ago, a couple of companies who can remain nameless here, decided to fund SCO to attack Linux via IBM, not because they thought they could win, but because the doubt hanging over the case would stunt commercial take up of Linux for many years to come (IMHO). In context, it's not how much money Ubuntu make off Linux now or in the future that's in issue, it's the damage they do to "Linux" in the process, that I find concerning. It's amazing how much damage waffling can do (!)
I know Ubuntu try not to mention "Linux" as such these days, but they are nevertheless known as a "Linux". When they put out applications that don't work or are buggy, people trying out Ubuntu then make the association that "Linux doesn't work".
Ubuntu claim their developers are doing this that and the next thing, making out that Ubuntu is doing all the work and is invaluable to the process (which is probably 180 degrees out of phase with reality) firstly gives the impression that Linux is fronted by a relatively small (200 people) outfit - which is not the case. Secondly people see "their" work being touted by Ubuntu as Ubuntu's work, I dunno, if you spent three years developing an application, then saw it included as part of Ubuntu, screen shots on their website etc .. saying it was all part of Ubuntu (with the implication they had developed it) - how would you feel ?
It's not any one thing they've done, and indeed it's only really become apparent more recently, but there seems to be an accumulation of "little things" which I would guess are driven by corporate strategy (or maybe just corporate attitude) that make me think they're going in an unhealthy direction for "Linux". (albeit the direction 'Ubuntu' seem to think is best for themselves)
For my part, I've been using Ubuntu fairly exclusively for 3-4 years and although I've 'tried' a dozen other distro's (and produced my own!) I've stuck with Ubuntu so far. I can tell you however the next time I do an install, it will be Debian and if it works as well as I expect it to, I'll be sticking with Debian moving forward. Not because Debian is technically better than Ubuntu (which would be silly, Ubuntu *is* Debian) but for the same reason I won't ever be loading Windows 7 onto a machine.