Yes, there are legitimate bigoted Star Trek fans. It’s the Internet. You can find an abundance of any extreme niche. I’m honestly willing to bet I could find an abundance of furry star Trek fans fairly easily also, despite furries as a whole being vanishingly rare in real life.
However it’s a lot more common to see legitimate criticism of Star Trek painted as bigotry, often by people who clearly aren’t really that big fans of the series.
You couldn’t criticize Discovery for the first year it came out without being called a bigot, and a lot of the people doing so would clearly have 0 idea about the greater Star Trek universe. I remember reading a multitude of comments calling Burnham the first female Captain or first black captain, saying how female senior officers were quiet and unassuming until Tilly came along, and a bunch of other shit that was objectively wrong.
I feel like most implied accusations of bigotry these days are low faith effort attempts to stifle criticism by newer fans who just can’t handle criticism. It’s exhausting and super toxic.
Finally Lower Decks is a grabbag of woke tropes but was met with widespread and is the most popular NuTrek among hardcore fans. That should tell you something more is going on.