Keep in mind that many capitals of US states are neither the state's biggest city nor in a central location.

But beyond that, historically, the panhandle of Florida was where the original Spanish colonies were founded. Tallahassee is between St. Augustine and Pensacola where the Spanish first colonized Florida. Places like Orlando and Miami were tiny in comparison to the cities and towns in the northern half of Florida.

Up until 1900, Key West was Florida's largest city. In 1890, it had 18,000 residents.

At the time Florida being ceded by the Spanish in 1821 the two largest centers of population were St. Augustine and Pensacola. As a result John Lee Williams of Pensacola and Dr. William Simmons of St. Augustine selected the former Indian settlement of Tallahassee. They scouted the 20 day trip between their two cities to find an acceptable place. They made a decision based on its location about half way between the two cities, a beautiful waterfall (now part of Cascades Park) and that it was an old capital of the Apalachee chiefdom. The town was founded the following year.

Also, here is a quick history from USF.