Uh...no. Back in the 90's and to a lesser degree in the early 2000's Paramount engaged in multiple scorch-and-burn litigations against the fans (including Rod Roddenberry until he bent the knee) for fan-run websites containing fan-made artwork, selling fan-made memorabilia, garage resin kits and other trinkets, etc. In fact, the "fair use" laws arguably came out of those early litigations back in the 90's with all the Trek-based websites popping up everywhere (including mine). We were all waiting to see where the hammer would drop next for the past 20 years.
Yes, Paramount and CBS throttled it back in recent years mostly because Trek experienced a massive dry spell since Enterprise tanked and they ostensibly needed the fandom to keep the interest alive without having to pay a cent of their own money for marketing. They did absolutely nothing at all back in the 60's and 70's because in their eyes, it was a dead franchise. Of course they wouldn't waste money to protect it back then! Now, since the Abramsverse movies have generated their own momentum in the franchise again and the creation of the new series (which conveniently seems to take place in the exact timeframe and prime universe of Axanar), Paramount and CBS is back to their old games. Axanar was a "low hanging fruit" that they knew would be an easy target to make a point, and an example, with much of the credit attributed to Peters' own arrogance thinking he could get away with it so blatantly!
Don't think in any way that I'm making excuses for AP or defending him. He fucked up...bad. And now he's going to pay the price, but with other people's money, unfortunately. But I call bullshit that CBS and Paramount are benevolent victims that magnanimously allowed everyone to run a free ride on their property all these years. It's just flat-out not true.