Trading stock is, and pretty much always has been, gambling. So your strategy should be the same as blackjack: Know the rules and know your limits. For the market, you should also be in for the long term, and always use limit orders.
Limit orders make sure that your buy or sell order are done exactly at what you want. Legally, the trade cannot execute unless it's at or below your limit if you're buying, or at or above if you're selling. That, more than anything else, protects you from small time fluctuations caused by HFT.
Going for the long term is really where the focus should be, though. HFT algos tend to fight cents or fractions of a cent(the event referenced here caused a 2% drop in the futures price, which came out to around 6 cents per : http://quotes.ino.com/charting/index.html?s=NYMEX_NG.H13.E&#... ). As a private investor, your focus shouldn't be on getting rich in a week. It should be making sure that the pile of money you have now gets bigger every year. Your limits shouldn't be the HFT-like fractions of a cent or tiny percentages, they should be in the 5-10% range for a return.
Also, since you're not going to win fighting HFT, don't bother. What they do shouldn't effect your overall strategy, because you're not in that space.