Most of the why it is explained quite well in the instance's sidebar:

We’re a collective of individuals upset with the way social media has been traditionally governed. A severe lack of moderation has led to major platforms like Facebook to turn into political machinery focused on disinformation campaigns as a way to make profit off of users. Websites with ineffective moderation allow hate speech to proliferate and contribute to the erosion of minority rights and safe spaces. Our goal with Beehaw is to demonstrate and promote a healthier environment.

Beehaw's approach involves a fairly aggressive content curation policy for their instance. This includes defederating instances (which they have done 387 times so far). If you agree with their philosophy this isn't a problem and is probably welcome vs a more laissez-faire attitude some instances have. They are also still very open compared to instances like Hexbear which runs Lemmy but has federation off (it looks like they are considering opening to some degree up at some point). They give two reasons for defederation in their docs:

First, if your instance houses or has a vast array of users that engage in hate speech, it gets added to that list:

We are simple with defederating: we do not allow hate speech, and we must consider our own limits when it comes to moderating. If an instance allows hateful speech or in our judgement has users who are too much for us to currently manage given the state of Lemmy, we defederate with it.

Second, some large instances (lemmy.world and sh.itjust.works) have been defederated because the burden on the admins and mods given current (incredibly primitive) tooling within Lemmy for moderation is too great even though the instance as a whole is not generally in violation of their hate speech policy. This is also a reaction to issues beyond the hate speech policy such as how users engage in the communities hosted on beehaw

The choice to defederate from an instance can also be based on our inability to effectively moderate that instance’s users. As of now, only two of our defederations are on this basis (lemmy.world and sh.itjust.works), and we hope to eventually refederate with both of them.

Finally, under the "inability to effectively moderate" justification they've preemptively defederated from instances that (likely mistakenly) had open sign ups and have had massive (likely bot) user growth. It seems they haven't updated their docs to reflect this decision yet, though.

Given their philosophy I think this approach makes sense, but I absolutely understand why this pisses off some people who want more of a free-speech/wild-west in the fediverse. While someone may be free to speak everyone else is free to not listen. You have no obligation to engage with those you disagree with, as much as those people may want you to.

Hope this helps.