The policy's critics have grown over the years, with the proliferation of the indie scene and the economic viability of just going to Steam, where updates are free. The most high-profile spat in recent times was between Microsoft and Fez developer Phil Fish, after a "nasty" bug was found that would wipe save files. Microsoft was going to charge its standard fee for Fish to update the game on Xbox Live, with Fish refusing to pay "tens of thousands of dollars." Fez 2 will not make its way to Xbox One.
With Sony's open courtship of the indie devs, not to mention the focus the company provided during their E3 press conference, Microsoft is on defense in terms of keeping the burgeoning scene happy in this era of digital distribution. The Xbox platform for indies (and their less substantial budgets) isn't what it once was back in the time of Limbo or Braid. But, you know, Microsoft is used to playing defense by now.
Update: Microsoft's Larry "Major Nelson" Hryb has just tweeted, "Microsoft eliminated fees for Title Updates on Xbox 360 Arcade games in April 2013."