Defenses have indeed, "figured it out". The top 4 rushing teams that run the Wishbone/Triple-Option—Georgia Tech, Air Force, Army, and Navy—are a combined 21-35.
However, they are successful running the ball with all four being in the top 6 in rushing in the FBS.
Teams approach this offense by containing the rush and funneling the play up the middle. This limits big gains and forces the offense to put together drives of 10-15 plays. Inevitably, a penalty or error derails a drive and they are left in a 3rd and long situation. This offense is not built to overcome long down and distances.
In response to comments below..
The legitimacy and effectiveness of an offensive system can be measured by the number of points it is able to produce. The object of the game, after all, is to score more points than your opponent. Wins and losses is an easy, but maybe too simple, way of judging this.
The four prominent Wishbone/Triple-Option teams have scored 1,334 points. That's good for 333 on average which would place them on the list of FBS scoring offense at 71 out of 134. Teams that have finished 71st in scoring offense in the past 5 years have combined for a win loss record of 29 - 33.
The last time a Wishbone led offense won a National Championship was in 1986.
Frankly, the speed of the game has made the Wishbone obsolete. Even ultra conservative teams like Alabama use offenses that look like a Spread in comparison to the Wishbone.