Update: Here is a copy of Mackey's blog, so you can get why he quit in his own words:

After much thought and consideration, I have decided to voluntarily give up my title as Chairman of the Board.  While I don’t expect this to impact the day to day operations of the company in any way, I wanted to share the reasons for my decision with you.

I have held the Chairman title since Whole Foods Market’s beginning in 1978, but the reality is that today it is merely a title with no authority or responsibilities.  The authority and responsibilities normally associated with the Chairman position were all shifted over time to John Elstrott, after he became our Lead Director back in January 2001.  Despite this shift in responsibilities, Whole Foods, along with many other companies with combined CEO/Chairman roles, has been targeted by corporate governance activists for several years now seeking a separation of these roles.

The members of the Board and E-Team tried to talk me out of giving up the title; however, I don’t believe it is in the best interest of our company or our stakeholders to devote any more time or resources to fight this misperception over a title any longer.  John Elstrott will now take the title of Chairman of the Board, which will accurately reflect the authority and the responsibilities that he has had for many years.  I will remain a member of the Whole Foods Market Board and will continue to passionately serve as CEO, hopefully for many more years to come.

I remain incredibly excited about the future for Whole Foods Market!  As the world slowly moves out of the deep recession we’ve been in for most of the past two years, our company is well positioned to resume our growth and to continue to fulfill our company’s mission and core values.  Happy holidays to everyone.

Bottom line: Not much changes, and he might not be as smart as we originally suggested.

Previous article:

John Mackey, co-founder, CEO, and Board Chairman of Austin-based Whole Foods is giving up his title of chairman. John Mackey will remain a member of the board of directors, and he said in a statement he does not expect the change to effect day-to-day operations, according to a KVUE report.

According to the Huffington Post, a shareholder activist group, CtW Investment Group, unsuccessfully proposed in March that the CEO and chairman roles be separated. In August, CtW called for the CEO's removal, saying that an editorial by Mackey opposing President Obama's health care plan damaged the company's reputation, especially among its left-leaning customers.

That editorial led to threats of boycotts and a local protest. The CtW group said that Mackey has become a "liability" because of his "indiscretion."

Voluntarily stepping down is the smartest move Mackey has made in several years. While I personally happen to agree with him, as a public voice of Whole Foods, it's not shrewd to entagle his political opinions with his public position. This move allows him to disengage from the company he founded and frees him to create a separate, politically-active, persona.

Whole Foods said lead director John Elstrott will become chairman. His current position will be discontinued.