Properly because they have too much money (don't laugh, there are a lot of big businesses out there that have this problem), or they need official support.
(Genuinely curious).
The interface is much nicer. Superficial, yes, but I like it, and so do the less technical folks.
Built-in integration to Mylyn in Eclipse (you CAN do this with Trac, but you have to install plugins and configure things within Trac).
Better reporting on workloads, productivity, hours, etc...
Easy custom workflows. This is huge.
Easy custom issue types with custom fields. Also huge.
Powerful user and group based permission schemes, which can differ based on project, and hooks up to LDAP or Crowd very easily. Also does SSO.
Can create tickets via incoming e-mail, and track replies to the same ticket.
Supports multiple projects on a single installation, with as much privacy and security as you want. We have many clients who each have their own project, can't see any other projects, but we can see all of them, etc...
Jira supports other code repositories, not just SVN.
I'm a Java guy, so having it written in Java, with access to the source, and built for extension, make it easier for me to customize than learning to write Python eggs.
Project Roles.
Of all the free stuff I've used, I liked Trac the best, but once I tried Jira I didn't look back. And with $10 licenses, it seems pretty good for small shops. Large shops should see it pay for itself pretty easily.
YMMV.