At least JS code in a browser is sandboxed. A Notepad++ update is just rawdogging an executable on your bare metal, perhaps with admin privs even, and hoping for the best.

First, it wasn't even the developer who compromised people, here; second, scripts in most cases are orders of magnitude less dangerous than a windows executable.

And, in many cases you can get some protection from a developer going rogue (or not writing perfect code), it's not an all or nothing.