There are a couple of points I would like to make, as I wrote my thesis on this topic. Prior to secession, U.S. troops were already in the state, as they were performing garrison duties at federal installations. Florida seceded on January 10, 1861 with these garrisons at forts in Pensacola, Key West, and St. Augustine (I may be forgetting a few). Troops inside Fort Marion in St. Augustine surrendered the installation and and what little garrison or supplies it contained. However, soldiers at Key West and Pensacola held out throughout the war, despite the pro-Confederate feeling in the town proper. So the idea that the Union invaded isn't entirely historically accurate, as U.S. troops remained in the state throughout the conflict.

Winfield Scott's Anaconda Plan called for the blockading of southern ports, so Florida was naturally an early target of U.S. naval operations. Furthermore, it was Robert E. Lee who recommended to Jefferson Davis that several coastal towns and installations be abandoned by Confederate troops. Lee saw that the geography of Florida allowed for an interior defense of the state at critical river junctions to prevent Union gunboats from penetrating deep into Florida and perhaps even Alabama or Georgia. Since Lee and the Confederate government viewed coastal Florida as strategically expendable, most Confederate troops abandoned these positions early in the war. By March 1862, St. Augustine, Fernandina, and other coastal towns were retaken by U.S. forces and remained under Union control for the remainder of the war.

Union controlled territory ebbed and flowed as politics and manpower demands from other Military Departments dictated the availability of troops. Despite this numerous small scale operations were conducted by both sides during the conflict, as Florida provided valuable salt, beef, and other supplies to the rest of the Confederate states. In addition, East Florida and other parts of the state were hotbeds of Unionist activity, requiring Union protection and Confederate retribution.

Florida also served as a testing ground for African American troops, with numerous Contraband and U.S. Colored Troop Units serving in the state. White and black regiments penetrated deep into the state along the St. Johns River, searching for blockade runners, freeing slaves, destroying cotton, and capturing livestock. In fact, skirmishes outside Jacksonville may be the first examples of White and Black Union troops serving in a long continuous and integrated line against a Confederate attack, far before Batter Wagner, Olustee, or other famous integrated events.

Ultimately, it was politics that dictated a major military incursion into Middle Florida. Lincoln's political rivals saw Union held parts of Florida as a perfect way to garner support for their presidential ambitions to unseat Lincoln. The idea was to break off a piece of Florida and have it reenter the Union, much like West Virginia, and allow it to vote in the coming presidential election. Since Lincoln was looking for options to "reconstruct" the South and also participate in the election, Lincoln's staff saw his rival's efforts coming and sent various officials to see about the prevalence of Unionist feeling in the state. Regardless of the military operations, Union held pieces of Florida could not even muster the necessary 10% of 1860 voters to be considered to re-admittance, under Lincoln's 10 Percent Plan. The military expedition to accomplish the plan swelled the state with Union troops and was launched in February 1864. This expedition ended in disaster at the Battle of Olustee, with severe casualties on both sides. Northern public opinion hated the "unnecessary" losses and many troops were pulled from the state.

Even after this removal of troops, U.S. troops continued to hold a considerable amount of territory and launched frequent raids into the state, reaching as far as Gainesville, Cedar Key, Appalachiacola, St. Marks, and other areas.

So to sum up, U.S. troops had a continuous presence in the state, Union controlled territory expanded early in March 1862 and ebbed and flowed as military and politics dictated. Numerous raids, skirmishes, and battles were fought across the state for various purposes. Florida saw some of the first cooperative action of White and Black regiments in the war that helped raise support among army officers for the use of black troops. Lastly, Florida provided valuable supplies and troops to other Confederate states and the Sunshine State's contribution to the war effort has long been overlooked by historians.

Sources: Buker, George E. Blockaders, Refugees, & Contrabands: Civil War on Florida’s Gulf Coast, 1861-1865. Tuscaloosa: University of Alabama Press, 2004; Nulty, William H. Confederate Florida: The Road to Olustee. Tuscaloosa: University of Alabama Press, 1990; Pearce, George F. Pensacola during the Civil War: A Thorn in the Side of the Confederacy. Gainesville: University of Florida Press, 2000; Schafer, Daniel L. Thunder on the River: The Civil War in Northeast Florida. Gainesville: University Press of Florida, 2010; Ash, Stephen V. Firebrand of Liberty: The Story of Two Black Regiments That Changed the Course of the Civil War. New York: W. W. Norton and Company, 2008.

First off they did invade Florida during the civil war. The fort at St Augustine was captured early on in 1862. Later in 1864 the union invaded the interior. You can google Truman Seymour (the union general) and/or Battle of Olustee. At that point they controlled Jacksonville and the river so it was no longer a useful port. I dont know how useful Jacksonville was in any event.

There were also small ports on the gulf side of Florida, Appalachiacola, Cedar Key and maybe St Marks that did serve as ports. However, these were shallow inlets and could not allow larger draft vessels into these harbors. So they had minimal value to the south.

I believe there was also some cattle production in the state had some value to the south. They had to use that one RR to get them north. I think that was the reason for the 1864 invasion. Again not a huge part of the civil war effort.

Florida did not have much of value in the civil war. Few people lived there. I dont know how much you know about the state, but at the time it was one of least populated states in the south.

Eventually the union blockade limited whatever effectiveness those ports had. Other than that, the state was not really that important in the war effort.