.ino is supported but you need to do some configuration and you need to use the verify button from the plugin (not the standard build from eclipse)The configuration you need to do is in the console if you have not configured.
I thought that the plugin is meant to help people who have used the Arduino IDE and recognised that it is not really good for developing more than some small sketch from time to time. But now I have learned that if you want to use it as a replacement for the Arduino IDE, you cannot simply install it, make required adjustments for the local environment (location of the Arduino IDE for example), copy your existing .ino sketches into it and start using it. This did not work (at least for me - perhaps my stupidity) - far from it. I had to enter a filename at some place (Arduino.h - this is an Arduino plugin, so why have I to place an Arduino related filename somewhere ? Why is this not a preset ?). I had to google quite a bit to find out that some other preset (external builder) gives error messages (make not found or something like that) and that a change to internal builder is required.