This depends on the situation. For small fleets, you probably don't need to worry. Hoshikos and Overseers in particular (or an Advent player with a Progenitor) can help you keep your capital ships healthy even while under fire. For big fleets, if you're not prepared to take capital ship casualties, then yes, you will need to keep them on the sidelines.
I play both ways. When my capital ships are kept on the side, I do not feel confident that I can protect them or that I can afford to lose them. When I have them in the thick of battle, I'm either confident that I can protect them (early-game), or I'm prepared to replace them if they die (late-game). It's a very difficult gambit, but it can be very effective.
Early-game, capital ships can survive with a combination of repairs and good maneuvering. Once large forces of LRF or bombers emerge, however, this is no longer easy. You will need to very carefully maneuver your ships to keep them alive. For most of the game, this is how it plays out, and capital ships are on the run. Late-game, this changes. Losing a 3000 credit capital ship is no longer a potentially game-ending event. With fleets of hundreds of frigates, it can become a normal operating cost, commonplace in those massive battles. You can actually afford to use your capital ships aggressively, especially if you make the enemy pay for taking them down. Because these late-game battles incur heavy casualties, it's also easier to raise new capital ships to higher levels to replace the dead ones. If you keep momentum, your capital ships no longer need to worry. It's not that they're harder to kill, it's that they're now easier to replace so it's no longer worth the enemy's time to go to such efforts to snipe them.