It's not totally separate. Paying taxes to fund orphanages, or to fund weapons of mass destruction, or actual wars that one considers to be intrinsically immoral, are radically different acts - and the moral act of payment is affected. To fund an orphanage might be considered an obligation by many, while to fund an immoral war might be considered a form of slavery and the funds taken under duress.

In other words, the morality of paying taxes is directly dependent on the legitimacy of the government demanding payment. And that legitimacy in part derives from their very actions, for which in an ideal wold they would be held accountable.