STO needs DirectX 11, that means you will need the latest Wine 3.0 or newer. Please goto POL => Tools => Manage Wine versions - and install Wine 3.0 or the highest version you see.
You can also just click "Install application" and search for star trek online. Follow the steps there, it should take care of everything.
But again, STO musst use Wine 3.0 or newer, it will not run with older versions of wine.