Why are people upset?
The news reports suggest that the warrants, etc. for the investigation were in order. The question is whether when legally investigating one complaint, evidence of another potential crime can and should be investigated. Other possible crimes include General Allen's alleged adultery (a crime for an officer), and the source of (unspecified) classified information in Paula Broadwell's possession.
How should the FBI decide when to pursue leads tangential to the case they are investigating? What if they found emails that appeared connected to terrorist activity? Or that Allen or Petraeus might become targets of bribery? Or that two consenting civilians had an affair (is this a crime?)? Where is the line drawn?
This all sounds a lot like when Clinton was asked a question that was not relevant to the inquire at hand, about legal activity between consulting adults, lied and then was impeached for that lie. Maybe the rule of law does not always lead to justice. Maybe we have become a crazy confused society in serious need of leadership to help us determine what is really important for our common good!