Ok... Not much information. A resignation and no reason for it given to the public. My guess is that he was fired. Why?
This snip from an article in Salon (written before the war) may put it into context:
"A key element of Perle's regime-changing plan is that it will be a tidy little war, since Hussein's empire is "a house of cards," as Perle recently told a PBS interviewer. He contends that an Iraq invasion could replicate the Afghanistan war; U.S. special operations units would assist rebels inside Iraq much the way the U.S. helped the Northern Alliance topple the Taliban.
"The Iraqi opposition is kind of like an MRE [meal ready to eat, or U.S. Army field ration]," Perle once told U.S. News & World Report. "The ingredients are there and you just have to add water, in this case U.S. support." (Eagleburger recently quipped about Perle's band of much-touted anti-Saddam rebels, "I think there are at least six of them.")
Two weeks ago Marine Corps Gen. James L. Jones called the idea of simply transferring the Northern Alliance blueprint to Iraq "foolish." And Baker wrote in the New York Times that regime-changing in Iraq would have to look an awful lot like the Gulf War, using hundreds of thousands of U.S. troops. Baker didn't mention Perle by name, but the target of this jibe seemed obvious: "Anyone who thinks we can effect regime change in Iraq with anything less than this is simply not realistic. It cannot be done on the cheap."
For years, though, Perle has argued it could be done on the cheap. How many American troops would it take to unseat Saddam? Before Sept. 11, Perle's answer was, in effect, zero. Appearing on ABC in 1998, Perle insisted all America had to do was supply "skillful" air power to protect anti-Saddam forces who, embraced by the Iraqi people and aided by military defectors, could topple him on their own."
(he's since updated his troop requirement to between 40,000 and 80,000)