I agree that the commentators were out to flay him, but keep in mind that McEnroe is trying to sell a book and therefore not adverse to making an inflammatory comment or two. His comment was actually made in the context of a discussion about Serena being the greatest tennis player ever, male or female. McEnroe's statement that she wouldn't likely beat a man ranked within the top 700 has no bearing on that discussion, because her stature as a player is not based on her results against men, given that she does not play on the men's tour. 
There's never been any question about whether men have the physical advantage on the tennis court! But anyone who plays or really follows tennis knows that what counts just as much, if not more, in tennis is what a player has between his or her ears. And that is especially where Serena has the advantage over most other players, male or female.