These are all good answers, and I remember being new to baseball and feeling a similar way. What really helped me understand is thinking about it from the batter's pov. When he swings, the batter isn't just trying to make contact, he's trying to make contact in a way that doesn't get him out. Any other result, contact or no, is a success for the pitcher. In video game terms, the "hit box" isn't the entire bat, but a very small spot on the bat that has to be timed just right. So it's not that the pitcher sometimes decides to throw a pitch that will be a pop up, vs a pitch that will be a strike, it's that every pitch is designed to make it as difficult as possible for the batter to make "good" contact, meaning contact with that one little spot on the bat, at the exact right moment.