The writer, who has indeed attacked software patents on previous occasions, omits a key step in his argument.
para 3 "Of course, that doesn't necessarily mean that Android infringes on anyone's patents.:"
This is absolutely correct. But it doesn't mean that it doesn't either. And without examining the facts (a matter requiring a significant effort of time and effort and no small familiarity with patent law) it is impossible to know a priori whether the patents have been infringed upon.
"It simply indicates that the companies in question have done the sums and decided that it is probably cheaper in the long run to pay licensing fees now rather than risk losing a long and expensive patent infringement suit and end up paying much more later. "
True. But without evidence and argument we still don't know if they settled because they (a) although they sincerely believed they were not infringing they didn't want to risk the legal process, or (b) they did believe they were infringing and whilst they would much rather not pay it was pointless to resist. All we can be confident of therefore is that (a) in either case their assessment of the risk has certainly been expertly evaluated by the best IP attorneys money can buy, and (b) those attorneys advised them to settle so they are unlikely to have been crystal clear it was blindingly obvious there was no infringement.
"In other words, these deals are mostly about the skewed incentives of the US patent system"
This is a false conclusion. This statement is not a reasonable consequence of anything that proceeded it. It is rather a statement of the writer's opinion of the patent system. He has twisted the argument, with no supporting evidence, to support his cause.
The fact is that from the material he presents (practically nothing) we cannot draw any meaningful conclusions about the state of the patent system. He and/or we may have prior opinions about the subject but this paragraph is just another opinion masquerading as an argument.