Mostly because Scalia wasn't making an analogy - he was challenging the government to define a limiting principle. If it is OK for the government to force someone to buy insurance at what point is it not OK for the government to force someone to buy something that it feels is important?
Scalia may have well have asked - if Congress thinks that forcing citizens to purchase yo-yos because Congress believes that every citizen owning yo-yos will prevent an invasion by little purple men from Alpha Centauri would that be Constitutional? If it is not Constitutional what is the distinguishing difference between the two cases?
In other words - at what point is Congress prohibited from telling someone that they must buy something? "Health care is special" is not a limiting principle because it opens the courts to infinite justifications around 'this market is special because:' type of arguments. For example, yo-yos are special because of their unique place in prohibiting invasion by little-purple men from Alpha Centauri.