Article I
Section 8.
The Congress shall have power to lay and collect taxes, duties, imposts and excises, to pay the debts and provide for the common defense and general welfare of the United States;
Also, the Second was written after the rest of the Constitution. The AMENDMENTS, clarify and modify the articles that cam before it.
The Second says quite clearly... "shall not be infringed." Do you need help with that one as well?
Which is in the main body of the constitution. The second amendment, along with the rest of the Bill of Rights, is an amendment. Congress powers are restricted by the amendments. The very nature of an amendment is such that it overides the original document, should there be a conflict. Although in this case, IMHO, there is not.
The clause you quoted just limits, although admittedly not much, what they can collect taxes for. They still are limited to the list of other powers enumerated in Art. I Sec. 8, plus a few more scattered about the Constitution and some amendments.