Did John Roberts Make the Affordable Care Act Unconstitutional?

All Bills for raising Revenue shall originate in the House of Representatives; but the Senate may propose or concur with Amendments as on other Bills. – Constitution of the United States, Article 1, Section 7, Clause 1

On Thursday the Supreme Court rejected Florida’s challenge to the Affordable Care Act.  Chief Justice John Roberts wrote the majority opinion for the court and made the legal argument for the laws constitutionality. Roberts rejected the Obama administration’s two primary claims; that the individual mandate was constitutional under the commerce clause and/or constitutional under the necessary and proper clause of the US Constitution. Instead, Roberts ruled that the mandate should be regarded as a tax. This was an argument the Obama administration had hesitated to make for months.

The President said on camera numerous times that the mandate was not a tax increase (this was as much a political calculation as a constitutional argument – one does not overtly telegraph large tax increases to the masses).

Here in lies the contradiction I cannot understand.