Kelv, this is a steroid era.
To give an honest answer to the question, I think alot has to do with money, and misconceptions. Players, minor league or big league, are investments, with millions of dollars involved. Therefore, restraints are put on the number of bullets a pitcher can throw in a game. When I played in affiliated ball the magic number was 100. Honest to goodness, we had pitchers taken out in mid-batter when a pitcher reached 100 pitches. Quick story for you guys. In low-A we had a pitcher working on a no-hitter, but he was punching out guys and working deep into counts. I can't remember the exact pitch count, but through the sixth the young man had around 85-90 pitches. In a normal situation, if the kid didn't have a no-hitter, he probably wouldn't have went out for the 7th. The manager actually leaves the dugout and calls the active farm director to ask if his pitcher can go over a hundred pitches to attempt to complete his no hitter. This goes to show you not only the strict limitations put onto young arms, but also the fear of managers and pitching coaches have of losing their job if they go over the pitch limit. Again, money plays a huge role in this. If a pitching coach leaves his starter out ther for 125 pitches and he blows his elbow out on his last pitch, you bet your you know what that coaching staff is getting fired instantly.
Again, the purpose of the five-man rotation is to help protect arms by giving the pitcher an extra day. There are millions involved, and unless in a playoff hunt, or actually in the playoffs or world series, an organization is not going to take a "risk" on their investment.
Do I think it's right or wrong? I don't know, I don't know a ton about the threshold of what a pitcher can handle. I will say that I don't think pitchers throw enough in pro-ball. Not necessarily in the game, I'm talking about things like long toss and bullpen sessions. I actually think pitchers are "pampered" or "baby'd" way too much, especially at the highest of levels.