If I remember correctly it has to do with that even though Pluto passes within Neptune's orbit, due to Pluto's inclination it doesn't come anywhere near Neptune's actual orbital path.
*edit* But as Astronuc stated, a sufficient perturbation could change everything.
The perturbation could just be the natural precession of the nodes. As an analogy, the nodes of Earth's moon rotate a full cycle every 18 years. Here's an animation: http://www.orbitsimulator.com/gravity/saros.GIF
All the planets have precessing nodes, even Earth which virtually has no nodes since its inclination is defined to be 0. The planets' nodes precess much slower than the nodes of Earth's moon (millions of years for a cycle is my guess). If Neptune's nodes and Pluto's nodes precess at different rates, then Pluto's nodes with respect to Neptune's orbital plane could one day cross Neptune's orbital plane at Neptune's orbital distance. Then Pluto's 17 degree difference with Neptune would no longer be an advantage.
But Neptune's 3:2 orbital resonance with Pluto will still protect Pluto from ever colliding. And it has a correction mechanism that keeps the resonance intact even in the presence of perturbations, ensuring that Pluto is never close to Neptune when it crosses Neptunes orbital plane. Here's is a page I made with an explanation and an animation: http://www.orbitsimulator.com/gravity/articles/pluto.html