Why do you suppose Martin O'Malley was booed for saying "All lives matter"?

I am only guessing based on what you wrote, since I’ve not heard of this event, but since this is a Social question…

My thought is that they may have responded from feeling that O’Malley was detracting, side-stepping, belittling, disagreeing, or not getting their message.

It reminds me of when I have been worked up about something that I care very much about, and feel that others in general do not care about nearly as much as I wish they would, and I am trying to passionately express my point of view, and then they make a counterpoint or sideways remark or other one-line statement that seems to not acknowledge where I am coming from. It tends to be quite frustrating, and attract at least some of my passion into anger against them.

Example:
Me: “Did you know that there are only about 3000 wild tigers left on Earth? People keep destroying more and more of the places where they can live.”
Herp: “Yeah, well, but people gotta live too.”
Me: “I dunno. I’m imagining a tiger eating you alive, and I can’t say I’d be too concerned.”

Because it comes across as dismissive. It’s like telling a cancer patient “yeah sure, everybody gets sick”.

The phrase “Black lives matter” does not mean that other lives do not (just as “Save the rainforest” does not mean “Screw all other types of forest” and “Save the whales” does not mean “Kill all of the other mammals”). His comment that all lives matters diminishes the importance of what’s been happening and the movement that has arisen to try to address the issue.

The same crowd gave Bernie Sanders a hard time too, despite his established long time record of fighting for civil rights.

Part of the learning process this early in a campaign is to determine ‘how’ to relate a message. Just like in a one-on-one conversation, ‘how’ one says something is just as important as ‘what’ is being said.