I've had to find a method for updating web.config with a SafeControl entry programmatically. Whilst searching I found this article by Mark Wagner http://www.crsw.com/mark/Lists/Posts/Post.aspx?ID=32
It updates all the web.config files for the farm web applications so I'll have to look at another method, maybe just use a straight forward Xml update.
We have a setup file that creates and adds features and also restores from a backup - this is so we have a clean installation for use. In some cases where features/solutions have already been added but this is a new site rather than rely on the creators to add the SafeControl entry I was looking at a way of doing it within the setup file.