According to multiple published sources, the straw that broke Theo Epstein's back in deciding to walk away from the Red Sox was this Boston Globe column by Dan Shaughnessy.
The Globe's parent company owns 17% of the BoSox, and the Globe has apparently been viewed of something of a house organ for Boston ownership to disseminate information. Epstein, reportedly, saw Lucchino as the primary source of the column, felt it was slanted against him in a way that indicated bad faith, and suggested that Lucchino wanted to make sure everyone knew who was really in charge.
Fascinating to see an organization that was on top of the world just one year ago seemingly imploding.