It might have been true at the start that Apple owed some success to the indie devs, but I'd guess most of them had their run and lost out to the big guys. Once the big guys came to town, the role of the indie changed forever. I would guess most indies don't show up on the charts as more than an blimp from time to time. Esp when you consider the number of indies out there. About the only thing I can think of for Apple to do is to make a separate section for indies to allow them to stand out a bit.
Not necessarily true to be fair. Indie doesn't just mean one guy coding away in his bedroom these days. Indie, as in not tied to a publisher covers a wide range of developers.
Some quite large, some small. Last I checked and I admit I may be out of date but springing to mind are, Realmac, 2D Boy, Zepto labs. Outside of iOS you have companies like Insomniac, huge developer but not tied to a specific publisher so technically still an indie. I could go on but I can't be arsed doing the research
Although obviously same rule applies, the bigger the indie the more attention they get and that's the crux of the issue.