The initial reason that dark matter was needed is because galaxies rotate slower than they should according to the visible matter that we see. This means that galaxies have more mass at their edges and that this mass is not visible (thus "dark matter"). See the Wikipedia article for other observations that dark matter is needed.
I believe that the reason that dark matter is not considered to be conventional black holes is that black holes are actually quite detectable, e.g. through their interaction with interstellar gas. It is also hard to think of a mechanism to create many black holes on the galatic edges that did not also create them in the body of the galaxy.
Or our understanding of gravity is subtly flawed, and the quantum problems do occur on the macro level, or there's a mechanism that we just plain missed.
See, I'll buy that there's matter that phases through other matter. I mean assuming it doesn't have a magnetic field, the chances of actually impacting another atomic nucleus are actually reasonably low, so it could reasonably pass through most semi-dense objects.
The problem is this matter is going to tend to collect in very dense objects - stars, planets, etc. The fact that the stars we observe seem to have roughly the correct mass if they're completely composed of conventional matter, and that the dark matter we're looking for outmasses the conventional matter significantly argues to me that the entire thing is missing something. I mean we ought to be taking mass readings of our sun and going "that's way, way, way denser than we'd expect" in that case.
I've never seen a good reason why that would happen that way. If the matter exists, its going to be sitting inside stars, and the stars just don't appear to be gaining ghost matter that way.