Wasn't Lewis more of a pit bond trader? When I read Flash Boys, I read it with the understanding it was kind of like reading a book from a Horse Drawn Carriage salesmen after Henry Ford released the Model T. He has a bone to pick, and his bias oozes into every word of the book. Are some of his problems with electronic trading valid? Absolutely! Is he horribly biased and lets that show in his writing to make a more "shocking" story? Absolutely!
There used to be a finite number of spots in the trading pits. If you didn't get into the pit, you couldn't be in on the trading and potentially millions that were made. Now the trading went from the speed of human communication to the speed of electrons moving over fiber optics. However, instead of a limited spot on the floor, literally anyone can buy space in exchange co-located datacenters. You and I could chip in and buy some servers to put in the Weehawken, NJ datacenter used for NYSE and it would be affordable. Electronic trading brought a lot of changes, some good, and some bad, but it is arguably more "fair" now than it has been for a very long time.