The theoretical justification behind IP isn't just "hey the government decided to come along and create some monopolies." You can model intellectual developments as positive externalities which are subject to free-rider effects that reduce or eliminate the incentive to create.
See, for example, chapters 4 and 8 of Boldrin and Levine's Against Intellectual Monopoly (Google to find the PDF), which presents empirical evidence that patent protections go beyond what is necessary.
"To sum up, careful statistical analyses of the nineteenth century's available data, carried out by distinguished economic historians, uniformly shows two things. Patents neither increase the rate of innovation nor are the best instrument to maximize inventors' revenue. Patents create a market in patents and the legal and technical services required to trade and enforce them."
My point is that a market in patents is not our goal, and absent evidence that such a market increases innovation (our real goal), there's no reason to have one. I don't think the evidence available supports the extent of the current patent system -- it might support a more limited one, but I'm not making a claim there.