Gene Roddenberry's views on a few key subjects were never truly known

Gene Roddenberry is an iconized person within the Star Trek fandom. He's often viewed as the benchmark for conversations over what should and shouldn't constitute a "real" Star Trek show. They cite him and his beliefs for why some things should be the way they are, or why some things shouldn't be the way they are. But the sad thing is that we don't know for sure if he'd approve of some things and not others.

We know he hated Star Trek II: The Wrath of Khan, one of the best films in the franchise's history, so if he'd be so polar opposite of what the fans like, how do we know that he would've supported something? We don't.

And that's something Rick Berman, Jeri Taylor, and Michael Piller, the creators and executive producers of Star Trek: Voyager had to accept. While the creator of Trek had women in positions of power, he also had the most prominent ones in positions no more powerful than that of "space secretaries" and nurses. While he was a progressive mind, he was only a progressive mind for his time.

So having women cameo as captains in the first few seasons of Star Trek: The Next Generation, a show he very much wanted to see changes made to before he passed, isn't a sign that he'd want to have one as the focus of an entire show.

In the book, "The Fifty-Year Mission: The Next 25 Years", written by Mark A. Altman and Edward Gross (via ScreenRant), Berman reveals that he never got to speak to Roddenberry about building a show around a woman, saying;

"We wanted Voyager to be different, so we made it different in a couple of ways. To start with, we placed a woman in command of a starship. It’s something we felt it was time to do and it gave us a new direction. Gene Roddenberry was never averse to the idea of having female captains in guest roles, but this was something that we never did get a chance to discuss with him. Jeri Taylor, Michael Piller, and I all agreed that when we took this on, that it was the next logical step for us. I’m sure Gene would agree."

It's a bold statement to say that Roddenberry would agree with the move, as there's no real concrete proof to that. He didn't want Patrick Stewart as Jean-Luc Picard, he didn't want The Next Generation to reuse older alien concepts and he's famously disagreed with a lot of the directions the franchise went after Star Trek The Motion Picture.

Going with Kate Mulgrew in Star Trek: Voyager to star was the right move. She was fantastic, but it's not fair to assume to know what Roddenberry would've liked.