If your players' batting mechanics are good, and they're still not hitting the ball, they are probably not seeing it correctly, or perhaps not following it right to the bat.
Here are a few drills that are designed to really keep your eye on the ball.
Balls and Strikes
Have the pitchers throw pitches and the batters just watch the ball into the glove and call balls and strikes. You'll be amazed at what batters think are balls. The best thing for good eyes are just seeing live pitching...lots of it, even if it is just being a batter while your pitcher is doing a workout. You can learn to read different pitches, and the pitcher gets better practice when there is a batter in the box.
Object
Try golf whiffle balls, small coffee can lids (thrown like frisbees), pinto beans, etc, anything that has them concentrating on a smaller than usual target and hitting something that moves, rather than moving in a straight line. This will improve their concentration and teach them to follow the ball all the way in.
Miss/Miss/Hit
Use a series of three pitches to teach them to watch the ball. The first pitch, the batter swings over the ball. The second pitch, swings under the ball. The third pitch the batter hits the ball. Repeat this drill until they can do it every time. After that, you can really fine tune this: Pitch 1- just nick the top of the ball. Pitch 2-Just nick the battom of the ball. Pitch 3- Hit it right in the middle of the ball.
Two-Ball Soft Toss
Get two different color whiffle balls (say red & white) or mark half of the balls with a different color dot. Works better with whiffle baseballs or even golf whiffle balls. Its easier to toss s maller balls plus helps hitters in focus and coordination. Toss the two balls at the same time (from same hand) and ask the player to hit one of them, either red or white. This helps players to coordinate, focus and react ti=o hit the correct color ball.
Pick a Number
Take 3 or 4 balls, write a number on each ball. The players job is to see the ball well enough to tell you which number is on the pitched ball.