Many people decide to do Pilates because they want to be strong and toned and flexible, which does require building muscle. While you may not get huge from Pilates, you will in fact be engaging in muscle tissue building resistance exercise. On the other side of the spectrum are people who simply want large muscles irrespective of function or flexibility. When the need for size gets to the point where people are searching out supplements and other steroids regardless of the ultimate health costs, there is a definite problem.
Remember that at the end of the day exercise exists to keep your body strong, functional, and mobile while satisfying the need for movement and fun.