While the technical details of the system might be up for debate, Flash Boys paints a broader picture of a broken global financial marketplace, run by institutions struggling to keep up with new technology and unable to craft good regulatory policy. A system gamed by investment firms (or more accurately, investment intermediaries like HFTs) whose advantage comes from exploiting these poor regulations and new technologies, creating market imbalances that affect the entire marketplace and generate incredible profits at the detriment of the investors to whom these firms have a fiduciary responsibility to.
The broader picture of a screwed up financial system, how it got this way, and who it serves was my biggest take away from Flash Boys.