Both the MSM and the Bush Administration, for different reasons, want to avoid this being seen as a Muslim terrorist attack on US soil
The MSM do not want people to decide, from objective evidence, that a bunch of brown-skinned non-Christian people are savages who need to be excluded from Western Civilization
Bush does not want to risk the rise of a movement to deport and expel Muslims from the US, or worse have al-Jezzera showing pictures and video of burning mosques, or people throwing Qu'rans onto bonfires. Such would inflame the whole Islamic world against US more than they already are, and endanger US forces in Iraq more than they already are
All of your reasoning is plausible. I'd like to add one more theory...
The MSM may be ignoring this on request from the FBI. Also, most reporters were saying this was a "dead" story last Monday. The AP has only released 3-4 articles which is what most reporters look for nowadays. As far as why the FBI might request it to be downplayed I see 2 possibilities; 1.) Matters of National Security - perhaps this event lead them to learning of the threats in NYC? or 2.) Perhaps they have found links and don't want to expose their ineptitude.
IMHO there is much more to fear from Americans thinking our gov't can't keep us safe from these things than Americans taking it out on Muslims and burning down mosques and such...