I think the issue is that because Jira offers the hope of a tractable customizable management process, it invites management to put in more process to improve their visibility of a project. This should not result in micromanagement, but it usually does. From a programmer's vantage point this is lose-lose, because your day to day tasks are weighted down by Jira-related bureaucracy, and your mastery of your schedule is continuously threatened by managers peering down from above to ask questions about this and that individual item on your work list.

I suppose its a necessary evil for an organization of a certain scale, but for whatever reason, I've chosen to work in teams that are small enough that we can dispense with JIRA all together.