The new policy is the result of recommendations from the Transit Effectiveness Project (TEP) tasked by MUNI to speed things up. As Freemark notes, the average MUNI boss or train travels at an astonishingly slow 8 miles per hour, so any action towards speeding things up is desperately needed:
"Those slow speeds are an impediment to easy mobility throughout the city and discourage people from taking advantage of transit.* The causes of the slow speeds are multifarious: The fact that most rail and bus corridors are shared with automobiles, the high density of stops, and, of course, the requirement to board up front. The result have been disappointing reliability statistics: Most services arrive at their destinations on time less than 80% of the time."
Freemark discusses the tools that allow all-door boarding to happen, like a universal fare card and card readers.