If downloaded from the developer site and you are using these miners directly with flags you specify, then everything is fine. These miners themselves can be run without ever showing a window or taskbar icon meaning that someone can write a program in seconds that can run this on your computer without you ever knowing it (except when you check why your CPU/GPU are running slow or acting up). And since crypto-currency is actual money that could be made, those who have control of thousands of infected computers can run these miners to mine on those computers on their behalf. This is why these programs are flagged. Not because the programs themselves are illegitimate, but because they could be and likely have been used in illegitimate ways.