Sync is by default turned off for google apps accounts. It can be turned on by following these instructions, then follow the steps here to add/manage the calendars that are synced. If you prefer, jump to the shortcut tip at the end!
1. On your iphone goto use Safari and goto http://m.google.com/ and scroll down to the box "Google Apps user" tap to configure your domain. In the pop up box enter your full domain name.
2. Now click on the sync icon that is in the highlighted area
4. Enter your user name (not a very iphone friendly sign in screen here but it works...) and sign in
7. You'll now get the manage devices screen and be able to choose your calendars...
** Shortcut **
Steps 1 to 5 seem to be driving the creation of the URL for your apps domain
which is https://m.google.com:443/sync/
If you want to enter the above address in Safari on your iphone replacing yourdomainname.co.uk with yep, your domain name.