Do you mean that the beat-it-during-break-in method is bad?
I went on a road trip with a friend of mine and his forum members. One of them was an middle aged gentlman (low to med fourties). He was a former pro. racer, being riding for 30 years, and he is very knowledgable about motorcycles. He has a Honda that he put over 100k and the engine, and it was running like the day he bought it.
When I asked how he did it, I found out about how he broke-in the engine. He broke the engine in 50 miles. Ride it very hard for 10 minutes, then let it cool for 15 minutes, and repeat. Change the oil and filter 50 miles later, and the bike is ready to go.

I know it is very controversially subject, but I want to know what you think? To baby the engine, or not to baby the engine?

I think it's a very heated debate, and IMHO, there are pitfalls at both extremes. Baby it too much and it won't seat as well as it possibly should, although the newest bikes get Nikasil coatings on both the bores and the rings, which should effectively eliminate the baby issue all-together. In his Honda's case, it was probably already pre-broken in at the factory on an automated rig, most likely before it ever went into the bike.

Beat it too hard at first and it can wear the mating parts too heavily and you'll get blow-by early in the engine's life, usually seen as a loss of some compression pressure and a degree of oil consumption.

The best method, IMHO, lies somewhere in between. You want the engine to get good and hot (not overheating, but all parts expanded to their full operating temp limits). At the outset, you want the detonation to last as long as possible to maximize the slide of the rings as they knock off the bigger pieces of the mating surfaces (which means lower in the RPM range), and then you want the pressure levels on the rings to maximize to finish the honing-in after the initial hone has been done (which occurs around torque-peak [around 8k RPM on a Kat]). Somewhere in there, you want to change the oil a couple times and the filter once. Finally, at the 600 mile mark, you want to drop the oil pan and physically clean out anything sitting in it (there will be a lot of bits bigger than you might imagine).

The three places I find people tend to err in their break-ins (again, IMHO) are:
(A) Take it to redline the instant you buy it and beat it hard continuously. I tend to find engines that got this treatment too early in the break-in process have the blow-by issue that I talked about earlier and the engine isn't putting out good power any more by 40k miles on the odo. These riders are also the ones who tend to wail their bikes before they let the engine get all the way up to operating temp in their daily riding habits, exacerbating the problem.
(B) Doing a couple hundred short -- one to four mile -- trips (run to blockbuster & home, run to the grocery store & home, run to the hardware store & home) with the bike cooling down inbetween each run. The engines aren't getting run all the way up to temp during the break-in, so the parts never get to expand all the way. These engines tend to have scorch marks on their cylinder walls because of the lack of proper mating.
(C) Doing the break-in on the centerstand and/or at idle. I've seen people bring home the bike, pop it up on the centerstand, put a fan in front of it, start it up (possibly locking the throttle into a specific RPM with some tape) and walk away for a couple hours. Aside from possibly overheating (definitely the case for oil-air cooled engines under most circumstances), there are other issues to do with loading the parts sufficiently that can prevent a healthy break-in this way.