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I think the belief that you need to be careful with the workload of young pitchers and gradually increase their innings is a well reasoned one.
First of all, just because something is healthy doesn't mean you can go from 0 to 60 in an instant. Running is healthy but if you are going to do a marathon you don't start training by running 26 miles. You have to steadily increase your workload over time. And if you are pushing your body to its limits (as MLB pitchers are), then that will take years.
This is especially relevant when dealing with young people who are still growing physically. What a person can do at 21 is not necessarily what they are capable of at 20.
Second, while people most certainly could safely pitch year round if they wanted just as you can lift weights, run and swim year round, that isn't relevant to professional pitchers. MLB teams aren't trying maximize how many pitches they throw in a year, they only care about what the players do from April to October. That means that teams are trying to push their pitchers beyond what they could sustain year round. It's possible to do this but it greatly complicates things and increases the chance of injury.
For example, while it may be best to have at least 6 hours of sleep a day, you could stay awake for 36 or 48 hours straight if necessary. But if you did that, when you did go to sleep you would need to be out for more than the normal 6-8 hours. And if you did this regularly it could be unhealthy. That's essentially what MLB teams are doing. They are red-lining their pitchers during the season which necessarily means they have to throttle back at some point.
It's not an issue of having only so many bullets in the gun, but rather that you can only fire the gun on full auto for short periods of time before the barrel overheats. And the more you fire on full auto the shorter the lifespan of the barrel. Since the consequence of overworking pitchers is often a severe injury that can put guy out of commission for a year or even end his career entirely, it makes sense to err on the side of caution.
So I'd say Major league teams now have the right idea, which means the main issue is determining where exactly you draw the line for young pitchers. The correct answer, of course, is that it varies with each individual player which really makes things difficult and puts more pressure on organizations to be careful.
*Small correction- Tim Lincecum threw only 177 innnings his rookie year