1) They are granted on small, low cost inventions, where others "invent" the same thing. The later should indicate that they are simply not novel and inventive enough to be patentable.
2) Tons of them are hidden inside a product, so you don't stand a chance of knowing what is patented and what is not.
3) Software patents are simply not needed to drive the software business: Without patents the products are copyrighted and that is incentive enough to keep producing software. There is no need to have a patent market around software as opposed to the drugs industry.
But what strikes me as a difference is that a in the drug industry a product more or less corresponds to one patent. That patent will only block copying of that single product - a specific treatment - not a lot of other product which happens to use the same technology.
Are we back a demanding a more or less one-to-one relation between products and patents? In software the small incremental inventions can not carry a product and shall therefore not be a patentable. In the drug industry a discovered drug is product and therefore patentable. But if one invents some algorithm of say making picture manipulation, and can make a business case around selling it as say plugings for Photoshop or Gimp, why should he not get the same patent protection as the drug company?