I see nothing wrong with it. Lots of things we're complimented for are often natural anyway, such as intelligence, personality (e.g you're really funny), body type and artistic or sporting talent.
As for just saying someone 'looks good' or their hair is really nice, those are still often natural attributes. As someone who doesn't wear makeup and make a big fuss over my hair, I'm pretty sure I've had received drastically fewer compliments regarding looks if it were all about effort and those kind of compliments can really cheer up a rough day.
Of course, some will find their natural beauty and the compliments that come with it a burden. Take Samantha Brick for example...