1.) Publishers do provide editing, etc. services that authors would otherwise have to pay for out of their own pockets. That may or may not be a worthwhile tradeoff. But, between forgoing and advance and paying for services, authors are probably at least a few $K out of pocket if they go their own way. To the degree that things like book tours/promotion/etc. are relevant--they often aren't--that can add to the difference.

2.) For, especially non-fiction, authors for whom books are more about boosting their profile than bringing in money directly, traditional publishers (rightly or wrongly) have considerably more cachet than independent publishing.

3.) This becomes less and less important, but independently published books probably won't be in book stores.