They asked for evidence and when the US said no they said they wouldn't hand him over.
Unlike his previous attacks, Bin Laden initially denied being behind 9/11.
Describing the faction of the Taliban that for a brief period gave Bin Laden sanctuary as a "government" seems like an unusual way to interpret the term government. It is the equivalent for us of having some bandit hiding within some cult in Maine or Kentucky and us describing that cult as the government of Maine. Also, as others in this thread have pointed out, those Taliban offered to handover Bin Laden if evidence was provided convicting him of the crime. It is interesting to compare our level of "conviction" of blame for some sets of people and willingness to accept collateral damage to civilians who happen to be around them, but when it comes to our own, even despite blowback and high levels of culpability, we deny the equivalence and block judgements even from UN courts.