There is the well-known principle, "money is fungible". This would seem to be something Canonical, as the corporate funder behind Ubuntu, is counting on.
Thus, even if you're not donating directly to Canonical, to the extent that Canonical can reduce Ubuntu funding due to these donations, you're still donating to Canonical. Only to the extent that Canonical has agreed not to cut back their own funding (or supply of services and product in kind) to these entities, does the earmarking have any real effect, and there's nothing in the article or other coverage I've read indicating that to be the case, here. (Of course, there'd need to be public reports on this along with independent auditing to be sure, as well.)
Thus, the real effect of the donations would appear to be two-fold:
1) They serve as a very real indicator to ubuntu/canonical of what people care enough about to be willing to pay for and to what extent, even when not absolutely required. That's seriously valuable information right there, and to the extent that it informs canonical's future direction of its own funds, could in theory not only counteract the fungibility issue, but actually boost the effects of donations several times over. (A well-known example of this in fund-raising circles is the contribution-match drives that often occur. These boost both excitement/PR level therefore driving larger contributions, AND the effect of any individual's contribution.)
2) Obviously, there's more money overall coming in, so more money to spread around, fungible tho it may be.
But, unless otherwise specifically stated (and as I've said, I've no indication that's the case, tho I'm following this a bit more remotely than you might be as being a gentoo/kde user, I've no direct personal stake in it, but there very well MIGHT be such statements that I'm simply not aware of), really, a donation to ubuntu must be taken as ultimately a donation to canonical, because money IS fungible, and to the extent that the various bits of ubuntu support themselves via donations and etc, canonical does have the flexibility to invest the money it would otherwise spend on them, elsewhere.