Well please prove me wrong but having talked to people like Roger Dingledine and Jacob Appelbaum in person and knowing a thing or two about how the Tor Project works, I have zero reason to think that this funding influences the security of Tor in any way, which is what "having its fingers in it" sounds like. The USA not funding the Tor project would, as far as I have been able to discover, not have changed anything about how likely it is that the USA or any other government has access to Tor users' data. If there are intentional bugs (bugdoors) inserted by any contributor, then those would be kept separate from any public funding it receives. Perhaps I'm not cynical, skeptical, or well-read enough though, so again, please point me towards anything that would suggest otherwise.

Then as for VPNs, they're again a very different thing. Funding research or a non-profit is very different from operating a commercial entity under a guise while abusing the trust anyone places in it. The comparison seems to me like comparing funding for general car safety or emission research with suggestions that the government operates one or multiple taxi services in order to learn who goes where. It's not that governments don't setup fronts or operate commercial entities under a guise ever, but rather that I have yet to hear of doing it for the purpose of surveilling random people (you have to get lucky in that anyone of interest signs up for yours, targeted marketing or no) that are not suspected of anything. Aren't fronts usually to enable targeted investigations or do specific actions unnoticed? Like, they might operate a VPN so it doesn't look weird if their secret operators use those IP ranges as well, but the main goal wouldn't be to spy on users (not saying they wouldn't do that on the side, of course, but it's getting more far-fetched).