I read the article -- very interesting -- but it doesn't fully make sense to me. I'm not an expert by any means, but I just don't see how doing only aerobic exercise makes you fat, or keeps you from losing weight. If you are burning more calories than you're taking in, then you lose. I mean, look at marathon runners, they are hardly fat! If the author didn't lose weight or gained while triathlon training, then somewhere, she was eating more than she thought, in my opinion. It's VERY easy to overestimate calories burned and very easy to underestimate calories eaten. I've fallen into that trap myself. If I go out and do a 12 mile run, I only burn maybe 1000 calories, because I'm pretty small and efficient at running. If I have a sports gel, one large bagel with cream cheese, a banana, and a gatorade (typical post-race fare), I've already eaten more than I burned.
I do think resistance training is very important and should be part of a balanced exercise program. Being strong is important, and it helps prevent injury. I think you have to eat enough protein to maintain and build muscle. But to blame cardio exercise for failure to lose weight -- I'm not buyin' it.