Sure, it may have been a little late to start and a lot less-attended than it was supposed to be, but the protest against DC's planned reboot did happen.
DC's planned reboot of its entire universe doesn't seem to be going over too well with the general public so far. In fact, between things like drastic character re-designs and breaking up Clark Kent and Lois Lane, it's safe to say that a lot of comic fans are getting pretty peeved. As a result, DC's Comic-Con booth was protested (and angry signs were taped to its sides) by frustrated fans.
It turns out that there was a scheduled protest that was originally supposed to happen at 2 PM on Saturday, and over 500 people said they would attend. As a result, Syfy's Blastr was on site to watch the protest unfold. However, the group didn't show up for about fifteen minutes (except for one poor guy who dressed as Superman and hung out, waiting for others to arrive), and then another dozen or so folks marched into the room and very loudly made their displeasure known about the upcoming reboot (like the Harley Quinn seen in the video here). Eventually, the group papered over at least one offending revised costume to with sarcastic signs.
DC Comics co-publisher Dan DiDio apparently wasn't around, so the company had no official reaction to the protest. That said, protesting something that DC has done several times before in this kind of manner seems more than a little silly. If fans are really upset about this planned reboot, then they should just not buy the comics; that seems like a much more surefire way to get the message across to the company executives.