As the director of one of the world's most well funded intelligence agencies one would expect that Petraeus would have been properly versed in all manner of security precautions, as well as knowing how to conduct clandestine affairs without coming under the scrutiny of his counterparts, yet this was not the case at all.
So, either Petraeus was a blundering fool, or there exists no privacy for anyone...
I'm guessing that Petraeus was no blundering fool.
His professional email was likely secure moreso than we'd ever see. However, directing agency resources to cover for an affair would be more blatant than someone discovering his GMail drafts folder. Being in charge of security and having excellent delegation / leadership - doesn't make one the technical expert.