I honestly believe that most passengers think highly of airline pilots. I just flew from JFK to TPA last night (as a revenue passenger) and when we touched down, quite a few people clapped. I hadn't heard this in this while.

People think Sully is Jesus' brother it seems, auctioning off his cap, book deal, etc.

However, in the trenches of the work-a-day world, it will always come down to money. People generally exhibit very little loyalty to an airline brand. As such, cost, route structure, availability of non stop options, etc are what people see. An airplane ride is an airplane ride. Whether that ends up being on JetBlue, Airtran, UA, AA, SWA, or whoever else is of little importance so long as the name is recognizable as a known brand.

To increase the percentage of crew wages to revenue, either costs must drop more in the face of fixed CBA compensation, or pilot wages must go up. Considering the present state of difficulty in the industry and the gluttony of pilots looking for work, neither is going to happen in the short term.

In summary: I don't think that passengers think lowly of pilots. Its just that the airlines must endure cutthroat competition to stay alive. The market will set prices/wages in an unregulated industry.