That is correct. However, the power bestowed on Congress, FDA, or whatever, to regulate commerce, is all coming from the commerce clause in the Constitution. At least in the early days, this power was so limited that Congress could only regulate interstate commerce. Over the years, this power was expanded, by the SCOTUS, ever since the NEW DEAL era. The famous case is the Wickard v. Filburn, in which the SCOTUS held federal government could regulate localized activity if such activity in its cumulative effect could affect interstate commerce. Many believed this was the origin that the commerce power ever became omnipotent as it is today. It went to the extreme in the Warren era. Rehnquist court reign it in but the damage was already done.
What CJ Roberts said is, although commerce clause gives the Congress power to regulate commerce, the Congress can only regulate what people do, not what people do not do. Requiring people to buy insurance is to regulate what they do not do, which is out of the limits of commerce clause. Kagan and Gin*****urg agreed to this particular point. Essentially, the Court told the government that when people buy insurance, you can regulate, such as regulating the price, eliminating discrimination of pre-existing conditions, etc. However, if people chose not to buy, the government cannot force them. For that, the law violates the Constitution. Granted, taxing on people not buying insurance is also a way to regulate the market and achieves pretty much the same effect, but that was another topic. It is bitter-sweet for BHO since he himself said repeatedly it is not a tax, but the law has to be upheld only if it is a tax.
I do admire Roberts as CJ, as a man with principles. He said that the Court must not be held hostage by politics. He gave his understanding and legal interpretation of the Contitution ahead of his political position. That is what a justice is supposed to do--to defend the Constitution. Whether this decision is right or wrong remains to be seen but I do dislike that fact that Congress now can regulate diet if it wants to (Roberts' words).