My dd is a little older, but I've actually seen her confidence blossom this year, esp. in the social realm. I worried alot about dd turning inward, low self esteem, etc.-I just haven't seen it at this point. I will say that positive social experiences seem to lead to more positive social interactions, and finding her "fit" w/her group of friends has been a big deal for her this year. I see your dd is homeschooled, so I'm guessing that's not an issue for her?
Participating in sports has been a good confidence booster-dd does one sport exceptionally well and another not well at all, but seems to really like both. Academics are hit or miss, so this is where I sometimes get a picture of lower confidence, but she's working through it.
I have to say, we have backed way off on our "helicopter" parenting, esp. in terms of choices about clothing, media, etc. It's not to say we don't have values-we do, and we talk about them all of the time. But we're out there with our discussion of valuing and respecting the choices dd is making, and reflecting w/her about mistakes, judgements, etc.
In terms of the negative comments--to some degree I think it might be the age. My dd has said that she hates her life a few times, and it revolves around leaving her possessions somewhere, or forgetting her homework, etc. Kind of dramatic, although the crisis is real to her. It's worth listening to though, because things can feel really hard at this age!