It's a program to get people new to strength training under the bar and out of the novice phase. I don't always agree with Rippetoe when he gets to running his mouth, but that area is what he knows best. The program works if you don't mess with it and eat and rest properly. If you insist on messing with the program the core principles even still work so long as you are resting and eating properly.
His main point is that for barbells the weight on the bar is the easiest factor to control while someone is getting stronger, so only increase that. Don't mess with your levers and angles like you do with body weight movements, don't do the lifts faster or with less rest and the same weight like you do with kettlebells. Just do five reps, rest enough, do five reps, rest enough, rest enough and then go on to the next lifts and do the same. In a couple days after you have recovered you'll be able to do exactly that with more weight. How much more? Sometimes a lot, sometimes less, but still more up until a certain point. And that point is much higher than most people think.