Not so much JIRA itself, but the ecosystem and culture that surround it. It tends to be corporate enterprise ware and a symptom of a top-down management driven structure. I'm not aware of any teams that chose JIRA on their own. It's also rather oriented to time tracking and micromanagement (or at least that's how my group is told to use it), leading to Bad Agile focusing on process not results.
It's not terrible to use, just mildly slow and clunky compared to other options like FogBugz or TFS.
My team picked JIRA after examining other options; we felt it was the best and most usable solution that wasn't a) Hosted or b) running on expensive alien software like Windows (we're a unix shop.)
It's not terrible to use, just mildly slow and clunky compared to other options like FogBugz or TFS.