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When Gene Roddenberry passed away, producer Rick Berman took over Star Trek. The franchise continued not because of his efforts but in spite of them.

Without going over the video, what I've gathered regarding why Trek fans seemingly despise Rick Berman:

He did not let the franchise explore things that strayed too far from what Gene Roddenberry had envisioned for TNG. It's why the principal critique of the latter series, that they weren't allowed to explore new themes and plots, is basically all down to Berman. Basically, he got a little too obsessed thinking about what Gene would have done with the franchise and used that as a way to avoid taking risks.

He was against the Dominion War in DS9 and wanted it over in a few episodes at most.

He didn't really let Voyager embrace its premise and reach its full potential. He also refused to innovate. Basically he (and Brannon Braga) just told the same stories over and over and over again. Stories that worked well the first time they were told in the 1980s/early '90s but by the late '90s/early 2000s were stale and repetitive, especially when compared to the burgeoning golden age of television. They came up with a good premise and launched them to great fanfare but then played everything completely safe. He in the end, tried so hard with VOY to replicate TNG and in doing so he stripped the show of the very things that made TNG special.

He fired Ron Jones because he thought his music was too "flamboyant". He told the rest of the remaining musicians that the music was to be "sonic wallpaper". In other words, the music should only be there for "being there's sake", which unfortunately was kept on for the rest of the Berman-era treks.

He treated Terry Farrell, Wil Wheaton (http://www.missionlogpodcast.com/the-one-with-wil-wheaton/), and Garret Wang like dirt. Wil wanted to do movies in the series break period and a few times during early season filming, asked for a bit of time off. Berman basically maneuvered the situation that Wheaton couldn't leave to do the movie work and at the same time was not used on the set for those episodes anyway. Garrett himself asked Berman about getting his character promoted and Berman said something along the lines of "then who's gonna play the ensign?" He also wouldn't let Garret learn directing (https://www.reddit.com/r/startrek/comments/e78dga/a_rant_about_rick_berman/f9wieec/?utm_source=reddit&utm_medium=web2x&context=3) and allegedly sexually harassed Terry Farrell.

He allegedly made the actresses wear padded bras, corsets, restrictive cat suits to accentuate their chests.

He made decisions based on the assumption that the audience wasn't ready for strong female characters or LGBT characters. These attitudes of his may have been more widely accepted in 1987, but by the late '90s-early 2000s, they were very dated, and he had fallen behind the times. Those attitudes put Star Trek in a place where it had become socially less progressive than actual modern times.

He had a "look" that all of the shows were required to keep, which limited the types of camera work and creative choices a director could make. As a result, the shows and movies all sort of look the same. He also banned cast members from working with the writers, which ultimately limited potential character growth.