Finaly, I found the solution. Browsing the isles of the local hardware store, I found an electricians toolbox. This toolbox is made by Custom Leather Craft, and its made from rugged nylon canvas. It has many small pockets, large pockets, and the middle is all open. Most of the pockets are very small, which typically works well, however I removed a few stiches between pockets here and there for some larger items.
There is enough room for my transmitter case, charger, tools, spare parts, rubber bands and more. Here are a few pictures of my flight tote.