Fan films won't affect the future of Star Trek.
Absolutely not true. TPTB attribute the return to the TOS Enterprise (JJ Trek) to the popularity they saw in TOS fan films.
Who are the powers that be you're referring to?
If you want to believe that Star Trek
fan films had a small impact on Paramount's decision to launch a big screen reboot of the original characters, that strikes me as plausible. But if you want to believe that fan films were anything more than a minor reason for Paramount's decision to sink $150 million (plus prints and advertising) on a big screen reboot, that's crazy.
After the collapse of Rick Berman's version of the franchise, a reboot was a forgone conclusion. CBS certainly wasn't going to let one if its most lucrative properties go to waste. That said reboot chose to use the most popular characters in the franchise (i.e. Kirk, Spock, etc.) is hardly surprising, either.