You may have a different view on it, because you know the mechanics and can say that's how it objectively works. Players have to make assumptions based on the effects, so until they have figured out the mechanics (if ever) their reaction is more emotional than rational. First time I encountered skill degradation I already knew it might take multiple days to increase a skill and I couldn't tell what the actual degradation value was, because I didn't remember what the previous skill value was. At that point I may or may not have succumbed to the temptation to look at the source code. ;)
Now obviously(?) I'm not saying I've got it all figured out. That people might consider an indicator "threatening" is a valid point and something that didn't occur to me, so there's that. I'm just offering my perspective, but at the same time I encourage you to keep making the game you want. I'd rather have a game with a couple things I'd consider flaws than a game with all the edges filed off.