Did that headline get your attention? It certainly got mine. Given Roberts' recent cautious statements about the "jolt to the legal system" caused by overturning precedents that are just a few decades old, it was rather surprising to see that he is ready to ditch Marbury v. Madison.
When I clicked through to the Los Angeles Times story over which the headline appeared, I saw that it was not merely an error by a copy editor. It was also an error by the two reporters who wrote the story (assuming they saw the edited version before it was posted). According to the lead, "chief justice nominee John G. Roberts Jr. said today it was appropriate for Congress to consider using legislative means to overturn Supreme Court rulings."
But according to the rest of the story, Roberts actually said it was appropriate for Congress, in the wake of Kelo v. New London, to consider legislation aimed at discouraging the use of eminent domain to transfer property from one private owner to another in the name of economic development. One bill, for example, would withhold federal community development grants from cities where such takings are permitted. This sort of legislation does not "overturn" a Supreme Court ruling, since it does not purport to elevate Congress' interpretation of the Constitution above the Court's. Like the Religious Freedom Restoration Act, it aims to provide extra protection for individual rights, beyond what the Court says the Constitution requires.
There may be constitutional problems with such laws to the extent that they improperly impinge on state powers; much of RFRA was overturned on federalism grounds. But there is nothing inherently problematic about restricting federal actions (including spending) in order to better protect individual rights, even when the Supreme Court says such restrictions are not constitutionally required. This is a far cry from asserting that the Supreme Court does not have the final say in applying the Constitution.