I'm not sure.
Schneiderlin has become a totem of fan frustration with his demeanour and performances on the pitch as well as his apparent poor attitude (according to the Ferguson training incident) off it. I understand why people are exasperated with him and by extension the season.
Booing some players might trigger a response. A "I'll prove you wrong" mentality.
Schneiderlin, I suspect, isn't such a player. He's more likely to try less or go into his shell. Which is not ideal. However, it is hard to feel sympathy or to want to support him. I'm not sure that would work with him either.
If nothing else, booing is cathartic for the fans. And it may encourage his departure. Worked for cleverly.