You have to keep in mind though that alot of time was spent developing the "Crystal Tools" which will be their main engine for games going forward. Things like the Unreal engine and Cryengine save tons of money for developers using them (and make a pretty penny for those leasing them). Square has no doubt spent an astronomical amount of money, but not just on FFXIII but a set of tools that they will be using to make HD high tech rpgs for years and years to come.
So even if they don't make a huge profit on FFXIII they may very well on whatever they do after XIII because the cost of making it will be so low using their new engine and tools. And if they ever decide to let other companies use their Crystal Tools then they will be have definitely made up the costs and then some.
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