you can update TopHat independently of your Galaxy version. If you are Admin, please go to the admin panel and upgrade your TopHat installation.
Also keep in mind that if you are referring to this (Galaxy Tool Version 0.9) version. Than your version is the latest version available. The Galaxy Tool version does not reflect the underlying TopHat version. Please click on the button next to the Galaxy tool version to see the underlying TopHat dependency.
I believe this is a misunderstanding of Galaxy Tool versioning.
The latest Tophat on usegalaxy.org is version 2.0.14. The version 0.9 is a version of Galaxy Tool...not the underlying Tophat software. You can see this details if you click on options/requirements