Strauss was a believer in the great books of the Western world and even in his life time was criticized for being "too Jewish" as were many of his students. Strauss also favored pursuit of an empire and supported religion but may have been a skeptic at best.
IMHO most of the criticisms are directed as his followers and their successes. I also believe, from personal observation, that many resent the "Jewishness" of the people Strauss mentored. Seemingly, if they had been Bohemians or Hollanders it would have been a more acceptible school of thought.
Yes,the column was an attempt to attack Strauss (with an implication he was a Nazi!), neo-cons, Christianity, and of course, the entire Bush administration.