This ignores the fact that the expensive, risky research is often funded by public money instead of by the pharmaceutical companies. So, the taxpayers pay for the research until it shows progress. Then it gets patented and sold to a large company which sells it back to the public for $1000/pill.
It's a pretty gross abuse of the original idea of patents.
The expensive, risky part of drug development is not the portion that is publically funded. Yay! You've found a compound that appears to shrink tumors when directly applied to them on glass slides.
Now, figure out what the correct dose is, how to get it into a mammal so that it's not metabolized into uselessness, how much you can safely give the mammal.
Now, start again with humans and hope you don't get to the final stage only to find out that it's not as effective as existing treatments or has side effects that will open you up to lawsuits.
Finally, once you've done all that, scale out the production of your compound such that you can prove that every dose meets FDA quality requirements.
To be fair the risky research side is relatively low cost. It's the development part - putting drugs through clinical trials that costs a hell of a lot. And its usually drug companies that pay for that.
It's a pretty gross abuse of the original idea of patents.