In any disaster, conspiracy theorists are quick to respond (with conspiracy theories)
Any time there is a big disaster in America, the conspiracy theories start flying almost immediately. In the case of the Boston Marathon bombing, conspiracies initially took a back seat to mob justice, as inexperienced and unqualified users on sites like Reddit leaped in and began identifying random strangers as the bombers.
Once this excitement faded and everyone sheepishly realized that they were dead wrong (and that our conventional law enforcement techniques are actually fairly useful when employed by traditional law enforcement personnel) the topic of conversation turned to What Really Happened and Who Really Did It.
For a brief moment, right after the bombing happened, some people instantly denied that it had happened at all. Many people claim that the bombings were a hoax, or that it had all been staged. Subsequent evidence and the overwhelming amount of first-person testimony has done nothing to quiet this crowd.
Next we have the inevitable cries of "false flag operation." This is a term which is used almost exclusively by conspiracy theorists. Here's how a false flag operation works: let's say that I sell anti-tiger insurance. "I don't have a tiger problem," you might say. I then sneak into your neighbor's house in the dead of night and release a tiger into their bedroom. I come back the next day and use the attack at the neighbor's house as leverage to get you to buy my insurance.
False flag operations are, like tiger attacks in suburban American homes, very rare. (In fact it is a phenomena which is almost exclusively limited to the fictional world of conspiracy theories.) It's easy to see why: false flag operations are a huge amount of effort, with a colossal risk of things going wrong. It also presumes that The People In Charge are so malevolent that they will cheerfully bomb a bunch of their own civilians in order to make a political point. Which, I have no love for the government, but seriously people.
The odious Alex Jones seems to be the main proponent of the current round of Boston Marathon conspiracy theories. Jones claims to have uncovered evidence that the bombings were staged, that the Tsarnev brothers were set up, and that the whole thing was meticulously constructed in order to take away more civil liberties from honest God-fearing Americans. (In other words: your run of the mill Alex Jones diatribe.)
As always, it seems that for some people, it's easier to believe in a vast and evil conspiracy than it is to believe that two guys with a pressure cooker could wreak so much damage on so many innocent people for no good reason whatsoever. Gotta say… I empathize.