The Taliban have always been a powerful force for manipulation in the country of Pakistan.The people had trouble surviving without some kind of input from them.With the flood aid people are more able to be independent and be free to live their lives so they may feel like they no longer need the Taliban.
One of the reasons the Taliban can get such a big foot hold in Pakistan as well as in other neighboring nations is that they can point to westerners coming in and damaging property along with hurting civilians. If we did more in the way of aid, we would be doing a lot to build a better reputation.
Smart aid given to other countries both helps relations with those countries and strengthens the US' position on the world stage. Aid given to Pakistan, without language that offends them (as happened in '10 with the military aid package) aid will be seen a gestures of friendship, strengthening Pakistani resolve to defeat the Taliban.
No, the Taliban in Pakistan would not be weakened by flood aid, because the money would likely be misappropriated. The money in Pakistan would likely be channeled to the leaders of the Taliban, rather than really used to help the people. Pakistan is guilty of doublespeak on the issue of terrorism, because they want us to think that we are an ally.
Sending flood aid into Pakistan wouldn't weaken the Taliban. In fact, such aid could be manipulated to the Taliban in order to benefit the organization. More flood aid should be carefully sent into the country to aid its citizens. However, we shouldn't expect such aid to weaken the Taliban in any measurable way.