The administration tried to argue it's constitutionality under the already overreaching commerce clause, Roberts did strike that down as being unconstitutional. His ruling on the constitutionality of congressional taxation protected a much bigger monster than Obamacare.
I understand the frustration of getting a ruling that says the Federal Government can FORCE us to purchase a product or service but think for a moment as to whether or not that was already taking place.... Medicare, Medicaid, Social Security, SSDI. We were already being forced to purchase these government plans for HC, retirement, and disability, but most Americans see these as merely a "tax" rather than government forcing us to purchase something. This new "tax" is merely an expansion of that (supposedly) unlimited constitutional power of the Congress to tax and spend.
Had Roberts ignored the "tax" side of the argument (even though the admin didn't bother making that argument) and ruled Obamacare unconstitutional on the grounds that the federal government cannot force individuals to purchase products or services (the minority opinion), the previously mentioned programs would have also been de facto ruled unconstitutional.Take a moment to think about that.
Such a reversal of previous court precedent would have created a firestorm of controversy and political upheaval the likes of which could hardly be imagined. I think that's what Roberts was trying to avoid in his ruling. I'm not saying I agree with his decision, I would have been deliriously happy to see the welfare state gutted and all of those "taxes" ruled unconstitutional to be tossed on the scrap heap of history, but I can certainly see where Roberts was looking and, therefore, why he ruled the way he did.