As it so happens, I have recently been informed that this is indeed the case, to some extent at least, so feel free to be surprised, but I'm afraid I don't think I can say any more about that subject now.
Anyway, as far as the WPI are concerned, they have not been receiving any major grant funding in the last couple of years, they are a charitably-funded institute set up by the family of an ME/CFS patient, and their interest is in studying and solving neuro-immune disease. If you take a look at them, it just seems to me a laughable idea that they are making big bucks out of all this. I'm pretty confident that they aren't as well paid as many of the peers in their field, and they certainly aren't as secure in their careers - they are sticking their necks way out, and everything I see tells me that they are doing this in the interests of patients, not in the interests of financial gain.
Of course, financial interests are there for all the players, but it's always interesting to me that the far more substantial financial interests of those working for state-funded organisations, and those well entrenched in the academic world, appear to receive far less scrutiny in these matters than the considerably poorer organisations like the WPI - I guess it's just a prejudice based on the fact that they're an independent institute and thus apparently 'private medicine', but when you look closer at it, this assessment of the relative financial interests seems like a nonsense to me. The idea that all the many doctors and researchers who are extremely highly paid to work in the public sector, in very secure jobs, are doing so out of altruism because they work in the state rather than the private sector, and therefore they're making some kind of noble (but highly lucrative) sacrifice...that sort of thinking is a pervasive myth IMO, because in reality many of the private physicians and independent researchers involved in ME/CFS are going way out on a limb for us when they have far more attractive career paths open to them. And as we know, without such people we would have absolutely nothing going on for us.
If you could cite any XMRV study that was funded out of an ME/CFS pot, or any ME/CFS research budget that has had money allocated from it to the study of XMRV, then you might begin to have a point. I'm not aware of any such example though, unless you count the WPI's own donated money.
As regards how it affects future research if something like XMRV fails to pan out, then I'm inclined to think that we really don't have very much to lose. It may be theoretically possible for ME/CFS research funding to get lower, but not by much. Again: the problem with research interest and research funding that you describe is the existing status quo before the arrival of the WPI, and it's hard to imagine that situation getting any worse. (That's the nice thing about this whole financial crisis: it doesn't seem to have touched us at all, because we don't have anything to cut in the first place - except for a load of money wasted on psychs, which would probably raise the biggest cheer of any budget cut going if it was all taken away).
I do of course think it's a great, great shame (to put it very mildly) that some of the other excellent ME/CFS research doesn't get more attention, more press coverage, and more funding. I just don't think the WPI can be held responsible for that situation, and if they weren't here and XMRV hadn't happened, I don't think the situation for that other research would be any better for it. In fact, if you look at some of the people who have got involved in the ME/CFS research field in the last couple of years, the opposite seems to be the case. So how XMRV will affect ME/CFS research funding in the medium term remains to be seen...