Sometimes, people discussing the topic try to explain the difficulty by proposing that it should be called “methodological atheism.” This is unhelpful.
True, MN promotes atheism. Unfortunately, then the discussion begins to revolve around atheism vs. theism.
But that isn’t what makes it a problem. Atheism could be true, after all. Then the fact that MN promotes atheism would be of no special consequence. The problem is that there is no way to test MN, as one commenter noted; it is merely an assumption. That is what makes it so attractive to crackpots. They thrive in areas where the basic assumptions cannot be tested.
It is why we have crackpot cosmology, for example, because fine tuning becomes a “problem,” rather than a research area.
As a rule, science thrives only when basic assumptions can be tested.