He was a proponent of the Alien and Sedition Acts that suppressed freedom of the press where it criticized the government.  Thomas Jefferson however, opposed it. 

Yeah, TJ was pretty cool with freedoms for citizens over the state.

Um... actually he was for individual states rights over that of the federal government which assumed to be in power because the people gave them power... and not the states (as Jefferson posed.)  So yeah... Jefferson wasn't really bad with all that compared to some federalists of the time... but the philosophy of where the government derives authority is all out of wack with what is commonly believed today.  When people say "the founding fathers believed this" I'm inclined to ask "which founding fathers?"

You're talking about a confederate government, like what we had before the Constitution (which created a federal governmen), right?

Not quite.  Jefferson believed in a federal government (he was a president.)  But he believed that the states had certain rights that the federal government could not violate.  He believed that the states held a certain amount of sovereignty, and could (although he never wanted it) secede from the Union.  But concerning the federal government, Jefferson believed that the States gave authority to the federal government.  Washington, John Marshall, A. Hamilton, and other federalists believed that the people gave the federal government the authority to rule.  And mostly (I think) because John Marshall was a chief justice on the supreme court, this federalist vision is what has been decided the Constitution meant... even though it doesn't really say.  But I didn't mean that it was a confederate government, that had been done away with by then.  Although Jefferson certainly had more "confederate" tendencies... but only when compared to Washington, Adams, Marshall, Hamilton and the gang.  And actually modern politicians who are all really incredibly federalist as opposed to Republican.

Ok, you're confusing government structures with government forms.

• There are 3 structures of government: confederacy, from which states voluntarily give a central governments certain powers, but essentially, the states are all separate entities(US under the Articles of Confederation, the EU, and the UN); unitary, from which all power is given from the central government (France, England, China); and federal, from which both the states and the central government share power, but states are a unitary government within their state borders (US, India, Germany, Russia, and Canada).
• Republics, democracies, democratic republics, kingdoms, socialism, democratic socialism, communism, and fascism are all different ways those structures are run.

Aaaaand on the federalist stuff:

• Federalists were in favor the Constitution before they included the Bill of Rights, which Jefferson and other anti-federalists said it lacked.
  
• Marshall, although a federalist, was key to creating a strong and stable judiciary branch to balance the other two branches.  He gave the Supreme Court the judicial review, which allowed them to overrule decisions of lower courts.  Because of this, landmark effects have been made to this country, like in the case of Gideon v. Wainwright, which verified that all defendants have the right to counsel in federal and state courts; Brown vs. Board of Education of Topeka, Kansas, which mandated that public schools be integrated; and Tinker vs. Des Moines, Iowa, which protected symbolic speech.
  

Sorry for the lecture, I'm preparing for an AP Govt test, and I'm trying to take every chance I get to review.

Yes, well... Jefferson was at heart more confederate.  However, he acknowledged the need for an overriding mediator in the federal government.  The difference in his philosophy and say Hamilton's or Marshall's is where the authority is derived.  Jefferson said that the federal authority was ultimately derived from the states--federalists said that the central government derived authority from the people as a whole.  Does this make a big difference?  It does whenever you start delving into matters of states rights vs. federal prerogatives.  If the federal government garners power from the people, then the states themselves are more subject to the federal government.  If the states are the givers of authority then the federal government has less wiggle-room to take state prerogatives.  It seems minor... but it really did make a big difference.  And bytheway, the "anti-federalists" became the Republican party--they figured it is better to stand FOR something than simply against it. 

You might enjoy the book "What Kind of Nation" by James F. Simon.  Some of my classmates found it boring... but I found it an excellent read about Jefferson and Marshall and their struggles with each other and the development of our nation.