One of the advantages of federation is that content can be distributed but still accessible, so on the one hand it doesn't really matter that there are three (actually more than that) rust communities on lemmy. On the other hand it can be confusing for newcomers and introduces a discoverability problem.
The factors I'd look at are how reliable is this instance, how well moderated is this instance, and lastly what are the rules of this instance.
On the first point lemmy.ml loses some points. It's heavily trafficed and struggling at the moment under that load. lemmyrs.org on the other hand is pretty new and low volume but so far seems stable. I can't speak to programming.dev because I didn't even know that instance existed until I saw this post.
On the second point I'm not sure there's enough data to go on other than to say that the main reason the quality of moderation matters is because a poorly moderated or controversial instance is likely to be defederated from other instances. While lemmy.ml is a fairly lightly moderated instance its importance as one of the founding and largest instances means it's unlikely to be defederated.
On the third point it seems like lemmyrs.org would have the least friction with the Rust community since it's ostensibly dedicated to said community and therefore should have no reason not to enforce the CoC of the community. I'm not sure what the rules of programming.dev are. lemmy.ml on the other hand has a fairly modest set of site wide rules. The rust communities would be free to enact more restrictive sets of rules however so ultimately as long as the rules of the instance aren't felt to be too restrictive by the community I'm not sure it actually matters.
Ultimately I think what will become the Rust lemmy community will likely come down to whichever one eventually gets the blessing of the larger Rust community. Once it's listed somewhere in the main Rust sites that will then be where everyone will gravitate towards. Until then just subscribe to all of them.
Consolidating on one Lemmy instance
[Disclaimer: Lemmy newb here]...