The GM should not listen to the fan base. He should make decisions based upon reports and recommendations of scouts in accordance with his plan for the organization. Fans are typically shortsighted, emotional, and ignorant of many facts and factors.
You're right. Fans can be emotional and very ignorant.
But you missed the point. He did, in a way, cave into fan sentiment. The fans didn't want to trade Reyes. I remember how fans even brought "Don't trade Reyes, resign him" signs to games. There were even articles in the NY times and stuff about how the fanbase didn't want Reyes traded. This was a factor to Sandy not trading him that mid-season, because the higher ups already knew they weren't going to re-sign him.
If the fans had kept their mouth shut, they could have traded Reyes and gotten a great prospect (another Wheeler so to speak). But in that case, the fans used their senseless emotion. This is what upsets me about this fanbase.