Weather occurs in the troposphere, which extends up to 65,000 feet (flight level 650) and tropical thunderstorms can hit the top of this layer - while commercial jets cannot. This means that jetliners cannot always fly over storms, and hurricanes in the mid latitudes will reach 50,000 feet. The height of the turbulent layer will get lower the further away from the center you are, but certainly no flight path will be routed towards the eye unless you happen to be aboard a Lockheed WP-3D Orion (nicknamed "hurricane hunters").