I have no direct work with I2C with Linux but I do develop embedded systems in Linux (Montavista)...
How are you doing right now? Still having problems? What errors are you getting? What kernel version are you running?
First make sure you have I2C built in the kernel or compiled as a module. View the .config file for your kernel and you should find something like this:
# I2C support
# CONFIG_I2C_CHARDEV is not set
that just means you have I2C in your kernel.
When you verify you have I2C in your kernel and it still doesn't work maybe its time to debug deeper
(bring out an oscilloscope / logic analyzer and tap your communication lines to the AVR).