Yes, T.O. the method lost even though it had the trifecta.

It loses most years but every so often there's a fantastic result. For example, when Vintage Crop won (so did the method) the trifecta paid $60,000. There's also been other good years.
And if the win section of the trifecta had been bet to Win on Betfair to collect $100 then the profit would be outstanding, with only one losing year. That was when Bart Cummings had his last winner (I can't remember the name of the horse...was it Viewed?).