The colors at flatuicolors.com are anything but easy on they eyes. Furthermore, in the flat designs I have seen you find out that a rectangle isn't a button when you click on it and nothing happens.
Well if you can't tell if something is a button or not, that is a poor design. If you design consistently, and treat all elements of the same type the same way, there would be no second guessing. It's not even hard to do, just requires a bit of planning.
It's up to the designer. But as long as it's used consistently through the design and it's different enough from other elements, your users won't have any issues.
