The fleet was made to combat the Decepticons many years ago and lead by the heroic Optimus Prime the fleet combated the Decepticons till they are defeated and survive the war against the sith.
In Darth Grievous's evil vision of the future the Fleet was destroyed in a titanic battle and the autobots last stand. Despite their resistance they failed to stop the sith from winning.
Venator Star Destroyers are large massive battleships larger than the minotaur class battlecruisers and are used for many purposes while the Acclamator is used to transport the non Flying Autobot troopers to various places. Minotaur class battlecruisers while not as large as their Venator counterparts are large but not massive are meant to deal with enemies with high armor and high hit points like the largest Sith battleships (the same way void rays deal with huge objects only the battlecruisers have multiple laser batteries that hit air and ground simultaneously) and finally armed with the Yamato gun which is only used on things that threatened their Venator friends like cruise missiles or Sith battleships. Both the Venator and the Minotaur can enter the planets surface to do planetary invasion but usually the Venator does space battles while battlecruisers assist the ground.
The Navy often requires fighter jets, Frigates, Corvettes and various starships to defend the capital ships and the cruisers. In honor of the transformers the fleet got Vikings that land to attack ground and transform back to jet mode to assist the battlecruisers and the star destroyers.
The Autobots also employ mass-produced Autobot Bodyform troopers that transforms into F-15 Eagles, F-22 Raptors, AH-64 Apaches, RAH-66 Comanches, V-22 Osperys, C-130 transport planes, C-17 Globemaster III planes, Pave Lows, F-18 Hornets and X-Wings. The autobot have small, secret ships with high-powered lasers in the front.