I'm not sure where there's more economic illiteracy: the DoJ or this forum.
Being a market leader does not a monopoly make.
A monopoly is defined as a barrier to entry in a certain market; that is, a single entity must possess the sole license to offer services in a certain market to be a true monopoly (e.g., the U.S. Postal Service, U.S. patent holders). The fact that Barnes and Nobles are at a competitive disadvantage to Amazon does not constitute a barrier to entry in the eBook market -- B+N are free to sell books and Nooks to whomever is willing to buy. If they can't compete, they have no right to demand that the government prolong their existence on their competitor's (and, typically the taxpayer's) dime.
As a matter of principle, the state have *no* business regulating who sells what to whom. Moreover, state intervention in the market also bears disastrous implications on a practical level. For all of their noble intentions, unintended consequences *always* follow from such state interference. This is a fact borne out by the immeasurable damage that anti-trust laws have done to many U.S. industries (including, sadly, the film industry -- in the old studio system, there were 2000 movies made each year and 200 producers; in the post-anti-trust studio system, 200 movies are made each year by 2000 producers).
Laying aside the ethical concerns of anti-trust laws, they are also fundamentally unnecessary. Imagined "monopolies", like Microsoft in the 90's, Wal-mart in the ought years, and Apple now, are inevitably eroded by a combination of time, technological advances and shifts in consumer preference. And yet the same economic illiterates who screech for anti-trust regulations time-and-time again conveniently fail to notice this phenomenon: when one dragon drops off the radar (Microsoft), they just seek out anther for Uncle Sam to slay (Apple). And the funny thing? The same anti-trust laws enacted to break-up a monopoly are eventually twisted to subsidize the prolonged existence of the market it was meant to break-up long after the above mentioned market forces have made it redundant (the railroad industry is a classic example).
Permitting a hive of bureaucrats to subvert consumer market forces as a means of fighting imagined monopolies invites nothing but disaster. It's hard to believe that most of you really want the same idiots who supply tax-payer funded military-grade weapons and money laundering services for Mexican drug cartels (See, "Operation Fast and Furious") in charge of micro-managing consumer markets.
If affordable eBooks are what you want, I'd advise taking advantage of this incredible library of free economics classics, available in many formats including ePub:
http://mises.org/Literature