Professor McClanahan is surely correct that the framers of the 14th amendment in no way intended to incorporate the Bill of Rights into the States.
The great trucks that have been driven through the “priveleges or immunities”, “due process” and “equal protection” clauses are shown to be contrary to the original meaning of the amendment in the books people have suggested previously in this thread.
I too did struggle with the same question you asked when I first learned about this: You said, “Did the Founding Fathers assume that States wouldn’t trample on people’s freedoms?”
I think it would be consistent to say that Jeffersonians were suspicious of ALL governments and their attempts to trample on freedom. But, that is precisely why they insisted on a federal government rather than a national government. A republic in which states retain sovereignty and can be different than other states is ultimately best for the people. States essentially “compete” for citizens, so if some state has outlawed free speech or denied due process to some, it is likely that people will try to free themselves from those areas.
Dr. Woods also has a lecture on the 14th amendment here where he mentions
the difficulty of the issue: http://www.youtube.com/watch?v=P56ZeBotFeA