The bank was not an agency of the state government, but a chartered private corporation just like any other business. Congress was not taxing the issuance of the charter by the state (an operation of the state government), but the issuance of banknotes by the bank (an operation of a private organization).
There is no doubt that Congress may tax for revenue purposes. But the federal government is acknowledged by all to be one of enumerated powers, and the problem here is that the Congress was using its taxing power to regulate private banking.
If Congress's power to tax is unlimited, so is its power to legislate. For the power to tax does, indeed, involve the power to destroy.