There's some disagreement in the U.S. Department of Defense over U.S. support for the Somali warlords and clans who are opposed to the "Islamic Courts" movement in parts of the country. The Islamic Courts movement supports the imposition of Islamic religious law. It's become somewhat popular in parts of Somalia because of the prevailing anarchy (and because some local warlords and clans find it a convenient way to increase their support). The critics say that supporting the opponents of the Sharia Courts bolsters Islamic radicals' claims that the US is engaged in a war against Islam, which has helped recruiting by extremist groups.
However, given the anarchy in Somalia, and the Islamic Courts support for Islamic terrorism, remaining neutral is not an attractive option. If the Islamic Courts, like the Taliban (and they are a lot like the Taliban in many ways), take control of the country, and allow al Qaeda to set up shop, how do you justify that neutral stance? Doing nothing is doing something, and it could be the wrong thing.