The difference is not about just scale.
While the rules were formerly unwritten, they were still well known to those in the fan film circles from direct communication with CBS, and it really came down to transparency to ensure that the money was only for equipment/materials such as building materials etc, and not for paying salaries and directly profiting off of it. When there were Kickstarters, this information had to be clearly written to satisfy CBS on the matter. Star Trek Continues raised well over half a million between their 3 crowdfunding campaigns, and had been in constant direct contact with people from CBS to ensure there were no issues. Despite running for years under the careful watchful eye of CBS, they've had no major problems because they've had nothing but respect for CBS and whatever requests have been made. They've even had several former Trek cast members involved.
Renegades also crowdfunded a lot of money over multiple platforms (at least 700k). I'm not sure of their money breakdown, but they also ran without incident despite the relatively high profile for a fan film due to the involvement of many former cast actors. Again though, they've been diplomatic in their dealings with CBS, and respectful of the franchise.
Axanar put themselves on regular salaries, and paid professionals to make a Star Trek film, even started selling all kinds of merch based on the film, and then had the gall to give CBS the middle finger as if they were entitled to do what they pleased, and then when slapped with the lawsuit, brashly proclaimed they would win and defeat the evil CBS. In the process they've killed off fan films, and I do directly blame them for that. Axanar didn't do anything "better", they exploited the generosity of CBS allowing fan films and even crowdfunding them, and then spat in their face when called out on their shady business practices and profiteering.
With the ever growing quality and technology available for fan films, it was becoming a slippery slope, and a finer line between fan film, and flat out unlicensed movie. Axanar didn't even care to try to respect that line.
All of that said, I agree with the stupidity of CBS/Paramount's guidelines overall (strange given they're still being moderately lenient with crowdfunding), and think it hurts them more than it helps them. Best case, I'm hoping they're not hard and fast rules of "if you don't follow this, we'll sue you", but more of a guideline of "stick to this, and we guarantee we won't come after you" and if you exceed their limits, it will be case by case of whether they'll nuke you. They might have felt they had to cover their asses better for any future lawsuits, with the guidelines now written plain and simple for all to see. Some of the rules I totally understand, while others are excessive to the point of quashing fan films altogether.
The backlash on social media over this from fans has been huge, regardless of which side people fall on with Axanar's part in this, so I don't know what will happen once the dust settles.
Let's just agree that Trek is in a bad place right now. There's plenty of blame to go around.