We are past the waves of FS ponies which featured Fluttershy unfortunately. As ponies are released in waves [i.e. for FS 2 or 3 at a time] it is the case that different ponies will be on the shelves at different times.
The most current wave of FS is Luna, Pinkie and Rarity therefore that is what you will find on your shelves [as you have]. If that's all you can find, then unless you find old wave stock you will at the moment be out of luck for Fluttershy.
Rainbow Dash is from a much more recent, and better distributed release, so you may find her somewhere. But if you cant find her in stores, I know plenty of people still seem to be finding her.
Honestly, I do think we will see the FS ponies re-released - they have been popular and they are a nice way for HB to keep releasing the main 6 and charge you much more money per unit. So perhaps you can post a want ad if you are super keen or maybe wait to see if and when she hits shelves once more.