Obviously, the costs for those trading more frequently will be higher, since their volume will be greater. But even here, the study estimates that fast traders might in total capture a profit of $32,510 in a single day of trading in Apple.
This is not a trivial amount but it is hardly an ocean of profits, given Apple's huge volume and high price.
The study also notes that dislocations are higher on days with higher volatility. This is no surprise, since high volatility days are associated with wider spreads.
There is another, closely connected argument made against high speed traders as well. That they can use this information to try to figure out what kind of trading strategies are being used at any one time and adjust their trading accordingly.
This can get close to being "abusive and manipulative" market practices as defined by the SEC, but it is hard to prove.
Read MoreSpeed trading firms get an edge over individual traders
I've said many times that I would support looking into charging some kind of excess message traffic for those who send in huge orders to buy and sell stock that are rapidly cancelled. Such practices, if done on a large enough scale, can certainly have the smell of abusive practices, but the devil is in the details.
What's the bottom line? If you are a long-term buyer, under some circumstances – particularly during times of high volatility – high-speed traders are indeed trying to scalp a penny on your trade.
Would I like to see fewer of these price dislocations? I sure would. Do I think this is some outrageous act of highway robbery?
Well, I'm not so sure.
What should be done about high-frequency trading? Let's start with two basic principles.
1) As a general rule, information should be available to all participants at the same time. If that involves instituting some kind of "speed bump" as the IEX currently employs, that is worth looking at, but only in the way described at the IEX. If there is simply a rule that says, "all incoming trades have to wait one second before they execute," than they guy with the fastest computer will still have an advantage, it will just be one second later.
2) Regulators should have the tools to detect abuse of the system. I'm afraid they don't have it now, but they are making progress. The SEC recently unveiled a new system, dubbed MIDAS, designed partly to look for manipulative behavior.
The SEC has put out bids for a deeper and more sophisticated tool, called the Consolidated Audit Trail, that would record every quote, every trade, every customer and would give the regulators a much clearer understanding of what is going on.
That will not come before 2015, but it will be a welcome development.
One final point about the 60 Minutes story: for a story that made the bold claim that the U.S. stock market was "rigged" and named as co-conspirators the New York Stock Exchange, the NASDAQ, all the brokerage firms on Wall Street, and a bunch of high frequency traders, you know what the story lacked?
Not a single one of these co-conspirators were in the story.
And, apparently, they were not even contacted. We didn't hear a single "we contacted the NASDAQ, and they refused to comment."
Not a single "we caught up with JPMorgan CEO Jamie Dimon and asked him about these activities, and he ran away."
Check back on CNBC's "Power Lunch" on Tuesday at 1 p.m. for an interview with Michael Lewis about his new book.
—By CNBC's Bob Pisani