Well, you're right. Taken in isolation, that fact wouldn't prove much about what his views were in 1803. That's why I put it in some historical context. Suffice it to say, even though it's true that the states weren't allowed to do anything that would conflict with the Constitution, it was the view from the time the BOR was passed, that the BOR didn't prohibit the states from doing anything; therefore no law that the states passed would have conflicted with it.
In order to have a conflict you need a prohibition. And it was the understanding at the time, that the way the BOR was worded, it did not constitute a prohibition on state action. The general view was that the Constitution had to specifically indicate that it was prohibiting states from doing something; otherwise it was considered a prohibition on federal action only. That's just how they read it.
The BOR's was intended to outline individual liberties that were NOT to be infringed by governments in the USofA at any level.
You could actually take that argument further and say that it outlined liberties people are entitled to all throughout the world ("all men are...endowed by their Creator with certain unalienable rights"). Nevertheless, the federal government was invested only with the power of upholding rights within a certain sphere. No one at the time of the founding thought to give it unlimited power of upholding rights. The people knew that power, even when granted for just purposes, was ultimately dangerous to their rights. They wanted that power to be balanced between state and federal governments, with the bulk of it going to the former.