Then click on 'Rules'
You'll see in my screenshot, below, that .svn and .git files are excluded (which was the default settings). I have also added two files which I never want to sync, which is local.xml and Config.php. These have server related information inside them.
My second rule ignores the folder called 'var'
Then there's the most important step. To tell transmit explicitly that you want to use the rules. This is not set by default, so you have to make sure the checkbox is selected at the top of the rule..