It has to do with the way power and incentives are configured within the project, and therefore what can be expected of the maintainers in the future.
For some people/use cases, the threat of developers rug-pulling a tool you depend on is not a big deal as long as it's good right now. But in many situations the tool which has less features but also less incentive to rug-pull wins out.
Anyone can "rug-pull" a project, whether it currently has non-free features or not. You can't retract already-published versions, but anyone can make non-free plugins or forks for existing MIT-licensed code (GitLab and Gitea are MIT).
I guess some might think that because they do non-free parts now they are likely to make more of it non-free later, is that the argument? If yes I don't really like this Minority Report approach to judging projects for what you think they might do.
> because they do non-free parts now they are likely to make more of it non-free later, is that the argument
Yes, that's one indicator of how the incentives are structured, though there are other factors to consider too - mostly regarding where the money comes from and who is involved in the decision-making.
Perhaps you find it dystopian that people make predictions about future behavior and use them to inform their decisions about who to trust. It's very common though, and is the basis for the concept of reputation.
For some people/use cases, the threat of developers rug-pulling a tool you depend on is not a big deal as long as it's good right now. But in many situations the tool which has less features but also less incentive to rug-pull wins out.