If you make a Star Trek fan film, feel free to make a profit from it, but be obligated to give CBS a share of the profit.
Um...no
You can't make any profit from it unless you specifically have a legal agreement with CBS to do so. CBS is not going to have the blanket policy to let anyone make a film using their property and just give them a set share of the profits. To do so would cause more legal nightmare for CBS than you can possibly imagine, not to mention multiple union violations etc..
If CBS liked a fan film and wanted to use it for a series, they would have to buy it and have everything completely re-shot under there controlled (and union'd) conditions. CBS can never officially support any fan film.
MGM has every right not to allow Stargate fan films, they own it. Some times studios will want put there properties to sleep and take it out of the public eye so that when they want to bring it back there is more of a fan 'hunger' for it.