Your flute it much better off in the wood case that it came in. It sounds like it is a French case? Those cases act like a vice on your flute and only grab it where there are no keys, so no lid is shut on top of the keys. I have seen more damage done to flutes because of improper fitted cases where the case closes on the keys.
Your best bet it to put it in a soft protective case cover that has a handle or a shoulder strap. Here are some really nice ones that I recommend.
http://www.wwbw.com/Cavallaro-Flute-Case-Covers-i85216.music
http://www.wwbw.com/SKB-SKB-1706P-Flute-Picolo-Carry-All-Case-i16475.music
While the Protec cases may look nice, they do close on the keys of your flute.