The idea of the patent system in itself is actually quite elegant. Government grants a temporary monopoly in exchange for the public disclosure of an invention. Everyone wins! The person issued the patent can more easily profit from their invention because they can work in the open. Society likewise benefits, no more secret guilds locking up knowledge, now everyone can see how it's done (and apply it once the monopoly expires).
As a social contract this really makes sense. The problem is that a lot of the patents being thrown around today only really satisfy half of that contract. A temporary monopoly is indeed granted, but the disclosure received in exchange is worthless information. I say it is worthless because no one actually needs to read that disclosure to figure out how to do it themselves with basically no effort.
Of the large companies, it seems to me that Apple is one of the worse offenders at exploiting the patent system in this way. Don't get me wrong, what they are doing is perfectly legal, but that doesn't make it OK. It does seem like Apple is following the legal rules and Samsung is thrashing around attempting to break them (perhaps feeling they have little alternative). But that doesn't mean that our legal system is perfect and cases like this will hopefully help us understand how it can be fixed to prevent this kind of exploitation in the future.