Well, I'm sort of the "yes and no" school with regards to that...
The Constitution was intended to delineate the limited powers of the Federal government, that is true. However, those rights are described as "unalienable". This means they are pre-existent to ANY government, and are inherant to the human condition, and their exercise and security is beyond the scope of ANY government.
Any government.
I think that perhaps they didn't delineate that these rights couldn't be abridged by the states or local goveernments, because they felt that those more local forms of government would be more directly answerable to the People, and therefore didn't have to be "reminded" that these rights were unalienable. They probably felt that it was, as they wrote, "self evident" that these rights were fundamental. Perhaps they had too much faith in the People to keep their local and state governments in line. Since all the states signed on to the constitution in Ratification, they probably assumed that the States actually agreed with the terms of the deal...
Unfortunately, political duplicity has been around for a LONG time, an it appears that this assumption (if it were made) was ill-conceived...
Legally, yes, I suppose an argument can be made that States and municipalities CAN pass laws that are contrary to the US Constitution. A weak argument, but the argument can be and has been made.
What is inarguable, however, is that states and municipalities do not have the MORAL authority to abridge these rights...
Unfortunately, morals and ethics have little place (or utility) in a court of law...