Here's the thing. We don't really know whether crowdfunding was the issue with CBS.
Maybe not, but I wouldn't be surprised if the amounts raised made someone at CBS sit up and say "Hold on a minute. Even if we don't mind what the fanfilm production company is doing with the money, we don't like the for-profit Kickstarter/Indiegogo/etc. making real money off our intellectual property".
Because the crowdfunding sites absolutely are making money of CBS's IP (because the campaigns wouldn't be able to be raising those funds without the draw of Trek), and I can't really blame CBS if they were not OK with that.
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