"I think it's a huge mistake because Zuckerberg should be a model, an icon, somebody that we should all be looking up to and aspiring to be," Draper told CNBC's "Closing Bell."
"This schadenfreude government is not appropriate — it's not the right approach."
Zuckerberg has faced harsh criticism in recent months for what some claim is failure to control the beast he created.
After reports revealed that political research firm Cambridge Analytica was able to access personal Facebook information of up to 87 million without their permission, the company has faced government probes and widespread concerns around user privacy and data collection. But Draper thinks Facebook is being unfairly "picked on."
"The point is to put your data up there and he's giving it to you for free, and so he sells ads against it and he uses the data," Draper said. "So what?"
Facebook, for its part, has admitted it failed to adequately curtail abuse of its systems and has made changes to its policies and advertising systems.
Zuckerberg has repeatedly said he takes personal responsibility and vowed to be more hands on with the data policies.
Draper also delivered an impassioned defense for disgraced health tech startup Theranos and for Tesla CEO Elon Musk.