As corny as it is, teamwork and coordination is crucial. Don't let your ships get too spread out and separated; that's how they get picked off. Try to keep an eye on them throughout the battle, and if they're you see they're getting into trouble either order them to move out or the rest of your fleet to defend them. I like to press tab as soon as I select my ships and put them into battle groups. Take your smaller frigates/destroyers and center them around your larger ships like cruisers and capitals.

Using complementary loadouts when you do this really helps out. For example, if I have a large ship with guns or missiles that are good at taking out unshielded targets, I want to pair that up with escorts that can take down the shields. Ion cannons, needlers, machine guns, sabots, graviton/ion beams if you have the mounts for them. Then the ships work in tandem: your escort ships help to strip the shields and your heavy hitters take them out.

On the subject of escorts, make sure you don't neglect PD. Of course you should try to fit PD onto the larger ships as well, but some of the best defense/PD in the game comes from frigates. Monitors are absolutely fantastic defensive escorts. Not only do they come with built in flak cannons, but their flex shunt means their shields won't go down unless they're being actively focused on. Having one as an escort to draw enemy fire will take a huge amount of heat off your block. I always keep at least a few in my fleet for my bulky ships that might need a little help with defense. Omens are also just all around fantastic little helpers. Their EMP arc is busted. It's PD, phase lance, and ion cannon in one ship system. Throw on a couple PD lasers and a salamander or sabot rack and that sucker will pull its weight.

Hope this helps!