An easy way to capture enemy flags is to go for the undefended ones. The majority of the action will be around just one or two flags and most people will use the default spawn option which places them close to the combat. The other flags will usually be completely undefended unless they are next to the bomber bunker or a plane. Even then, you'll often just get one camper waiting for a chance to grab the goodies and you can either wait for them to leave or sneak up and melee them.
The easiest way to make use of this strategy is to grab a boat, either off your carrier (press Y and use RS to pick it as a spawn point at the deploy screen) or off the map (like on the lagoon on Wake island). Have a look at the map to find an enemy flag far from combat and scoot over there. Try to find cover when you get to the flag because as soon as the enemy sees their flag disappear you can probably expect visitors or sniper attention.
One of the easiest places to do this is Wake island. There are boats on either side of the lagoon and most of the action will center around the airfield in the center. You can go back and forth across the lagoon taking over flags. If you have the sniper loadout you can sit across the lagoon in safety and snipe at the enemies who arrive to recapture the flag (why do people stand still when they run up to the flag?). Not only will you boost your score by 30 every time you capture a flag, you'll also be helping your team to win the game by keeping your flag count high (so the enemy point bar drops) and pulling enemies away from the front lines to recapture the flags you just stole.