Medical marijuana is state issue

Federal supremacy in laws is limited to laws which are within the mandate of the Constitution, which is very specific about what powers are granted to the federal government and which are reserved for the states and individuals.

When Congress wanted to pass alcohol prohibition they had to first pass a constitutional amendment because the constitution didn't grant that power to the federal government. When the issue of prohibiting marijuana came up they decided to make an end run around the Constitution by making it a tax issue: you couldn't deal in marijuana unless you paid an outrageously high tax, you couldn't get the tax stamp unless you had the marijuana in hand, and it was illegal to have the marijuana in hand unless you already had the tax stamp. Catch-22.

This was challenged in 1970 and the Supreme Court ruled that the law was unconstitutional because it violated the Fifth Amendment: in order to satisfy the law you had to incriminate yourself. Congress immediately passed the Controlled Substances Act, which attempted to prohibit drugs based on the Commerce Clause of the Constitution which allows the federal government to regulate interstate commerce.

This was challenged in 2006 by two Californian medical marijuana patients who made the argument that since their medicine was grown in California, never moved out of California, and wasn't bought or sold, there was no interstate commerce (or any commerce, for that matter) and didn't fall under the purview of the federal government. The US Supreme Court shot it down on the specious argument that their homegrown marijuana somehow (magically?) affected interstate commerce in marijuana and was, therefore, something over which the federal government should have control.

Federal supremacy turns on whether or not the law involved is a part the limited power granted to the federal government under the Constitution. The issue is not whether federal law trumps state law: it does. The issue is whether or not the Constitution grants power to the Congress to make laws in the area of drug prohibition under all circumstances. If the Supreme Court had ruled in favor of the two Californians it would have brought into question a whole body of federal law rooted in the Commerce Clause. It's not surprising that the Supreme Court would refuse to open up that can of worms.