1) That PACER charges for people to access "the law." As the article points out, "judicial opinions are free" on PACER. They're also typically published as PDFs on the courts' websites.
2) That the "costs of storing and transmitting data have plunged, approaching zero." That may be true, but the cost of maintaining and upgrading an electronic filing and access system have not approached zero. And there is no free off-the-shelf system that does what PACER does.
3) That PACER is meant for access to public records. PACER is a read-only view of the courts' filing system for lawyers and the court to use. Because lawyers use it, lawyers pay for it. (Individuals representing themselves pro se can use it for free.) It may indeed be desirable to make these legal filings publicly available through some system. But PACER is not that system.
The issue is not really that "PACER should be free," because it's quite reasonable to charge lawyers a fee for a service they use that's provided by the courts. What you really want is something like the various "Open Government" searchable data sites that are out there. PACER is not that system--it's not easy for the public to use, it's search features are primitive, there is no way to do bulk downloads, it's running on the same systems as mission-critical ECF filing functions, etc.