One possible explanation (that supports the author's main thesis) would be that three out of five of these are unlikely to be the main language for a project, but rather a supporting language. In other words, SQL and shell are just as likely to show up in a green-field project as in a brown-field project, because we still use SQL to communicate with database same as 20 years ago, and we still use shell scripts to tie it all together.
No idea how one would test this hypothesis, however. And I still don't have an explanation for why Scala and Haskell are both loved and hated.