Sen. Murkowski's statements regarding the fact that transportation funds earmarked for Alaska bridges (Knik Arm and Tongass Narrows) could only be used for roads and bridges in Katrina relief is part of the story. The other part of the problem with diverting these funds from Alaska to the Gulf Coast is that it represents a deviation from the normal federal aid-to-highways formula.
As I understand it at least part, if not all, of the funds earmarked for these Alaska bridges are part of the regular formula distribution of federal-aid-to-highways funds to the states, including Alaska. The only thing different about the Alaska bridges and other "earmarks" is that Congress has made the decisions with regard to allocation of federal funds instead of DOT/PF. To remove these funds from Alaska would violate the formula distribution and open the door for more states to face reductions in their formula federal aid funds as well. For this reason it would seem to be very difficult for Congress to mess with any state's earmarked funds as it could open the door for raids in any state.