I don't think it is fair to call the bombings a "false flag." The bombing was a terrorist attack on a major American city. Although, I believe that this was probably an isolated incident, it does not hurt to be more cautious until the suspects are arrested and convicted, they may strike somewhere else.
Are false flag operations a real thing? Yes. Go ahead and wikipedia them right now. But the Boston Marathon bombing was certainly not one. Is there an upside to the Bombing for anybody in the Government? For sheer practicality, what would bombing the marathon accomplish? Terrify an American City for a few days? Add security to next years run? Without a definitive benefit to the bombing, there is no point in debating government involvement in it.
I suppose it's physically possible, but it sounds like a wild conspiracy theory to me. I do think it's possible that the government and media will twist the incident to serve their own ends, but that doesn't make it a false flag. That's a bit too outrageous of an idea for me to consider.
While numerous conspiracy theories have been floating around regarding the likelihood of this being true, I dearly hope that it was not. It's far easier to consider it the work of a deranged person than it is to hold the government accountable. Certainly, there is a possibly that it was, but that opens the door to many other possibilities that this country is not prepared to handle.