Patent are useful for laboratories when they spend a lot of money finding solutions which need a lot of scientific work: for example, finding an efficient molecule to develop a drug that treats a certain disease, requires work, while making that molecule is just a matter of chemistry.
On the other hand, a software idea just requires the work to implement it, something that is just plain different.
In one case, it requires work to find a solution, in the second it requires work to make it work.
Patent protects research that finds stuff, NOT the people who make them. The protection for people who makes stuff is called copyright, which is completely different. This way, patents are much much rarer than copyrights.
The problem with patents is this:
They are over used anyways, because there will always be a debate about the expertise necessary to validate something that can be patented. Just look at all those numbers that appear when you start up adobe reader: it didn't prevent Google, Foxit and other application to write their own PDF converter. Also TeX seems to be able to produce equal if not superior quality documents.