Madison believed that the government should have the power to tax American citizens as much as it wanted because of what those taxes would be used for: national defense, the protection of the people's rights and freedoms, and any other services they might require. In other words, the United States government had a duty to its citizens, and it needed money to fulfill its obligations to the people.
In Federalist Paper 45, written in 1788, Madison addressed the federal government's power of taxation directly:
The change relating to taxation may be regarded as the most important; and yet the present Congress has the complete authority to REQUIRE of the States indefinite supplies of money for the common defense and general welfare, as the future Congress will have to require them of individual citizens.
While both Madison and Henry believed in the importance of individual liberty, Madison thought Henry's take on the concept was too idealistic. Madison was most concerned with how the United States would act on the world stage—and the word "united" for him was key. He felt that the United States needed to present itself as a tight-knit, unified country, not a conglomeration of factions that may or may not be on the same page policy-wise. For Madison, the way to do this was to have a centralized government that would represent all of America and speak on its behalf in global discourse.
Additionally, Madison believed that a representative democracy staffed by a handful of prudent men (and it was all men in those days) would ensure that decisions were made for the common good and not in the interest of only one of the factions being represented.
In the same vein, Madison strongly favored the checks and balances system enabled by the separation of federal power into three distinct yet equal branches. Henry, in contrast, believed power should stay with the states, and the conflict between he and Madison was a hint of the far greater and more brutal civil conflict that lay ahead for the young United States.