The problem, as the article points out, is that many of these companies may be misclassifying their workers. Uber has been sued over this[1], and most recently, Handy was sued for a variety of labor violations, including misclassification[2]. Ironically, I pointed out that a description of Handy's operations published in an article raised questions about classification a few weeks before the lawsuit was filed[3].
There's nothing wrong with self-employment (it's great), but most of these startups in no way, shape or form represent the true "1099 economy." It's a total misnomer.
http://nymag.com/daily/intelligencer/2014/09/silicon-valleys...