The reason everyone believes in dark matter is WMAP and other such surveys - the CMB is much more difficult to explain without some non-baryonic mass.
Regarding your points:
1) That paper only said that, using an oversimplified model (spherical symmetry), accretion rates depend on whether the inflowing particles are relativistic. It makes no claim that the existence of dark matter would imply different black hole accretion rates from those we observe.
2) Modified gravity was a big thing some years ago, but it looses support every year. Moreover, it is an alternative theory to dark matter, and does not in any way constitute evidence against dark matter.
3) CoGENT, like all dark matter experiments (and there are dozens), is sensitive only to certain parameter-space regions, and no one experiment is thought to give the definitive word on dark matter, unless a reproducible, positive result is given.
If you want to see more direct, visual evidence that baryonic matter does not necessarily coincide with the dominant sources of gravity, modified or not, take a look at the Bullet Cluster, where the X-ray emission from the intracluster medium (which contains most of the mass of clusters by the way) clearly does not coincide with the gravitational lens map.