Oh, there's no doubt the Commerce Clause allows Congress to pass health care legislation. I can see how an individual mandate as a part of that legislation may prove problematic, however. With this bill it is not just economic activity that is being regulated, but inactivity. Does the Commerce Clause allow the federal government to regulate such inactivity? I think it's a pretty fair question, and I don't have the case law to say one way or another.
In my home state along with others, car insurance is mandatory to be on the roads.
I can see a valid argument being made that health insurance is needed in this country.
The car insurance rationale is because of the idea that people at fault for car accidents should have insurance to pay for the injuries to life and property they caused. The legitimate governmental interest would be the ability for people to pay for that. Government cannot sustain a citizenry of drivers that cannot pay for their faults.
A similar argument could be made for health care. All people need health care so that when they do get injured, the bill isn't taken care of by the guvment, but the insurance policy. I can't see the conservative justices saying that's not a legitimate interest.
There could be an equal protection argument made, but that would most likely fail also through the legitimate governmental interest framework as well. Any classification (in this case, insured vs non-insured) would be held up to lesser scrutiny unless the plaintiff could make a claim that the discrimination was related to race. Race is pretty much the only real way someone could make a viable equal protection argument and have it win past a legitimate governmental interest argument. The standard is a lot higher when dealing with race-based classifications.