When someone helps out someone else, they are aiding them. However, if they are too far gone, there is little the other person can do to help that person. The Pakistani military is like the person that is too far gone. The US can't help them because they can hardly help themselves.
The problem with Pakistan is that we have made a deal with the devil: we need to move troops and supplies across their territory in order to persecute the war in Afghanistan, however this puts us in a weaker position since we need them. Pakistan is a very unstable state still characterized by coups and other political instability, which is dangerous for a nuclear-armed state. Since we do not want to destabilize Pakistan by having their military engaged in a civil war with the Taliban and other insurgent groups, it is probably better for U.S. troops to fight these groups directly, thus bringing their ire on us. Ironically, this is likely the lower-risk solution, though not a perfect one.