In the books of Jules Verne, the protagonist with the most questionable ethics is…

• Doctor Antekirtt
• President Barbicane
• Ilia Brusch (from the Danube Pilot)
• Phileas Fogg
• Captain Hatteras
• Kéraban the Inflexible
• Professor Liedenbrock
• Captain Nemo
• Hector Servadac
• Zephyrin Xirdal (from the Chase of the Golden Meteor)

Maybe I should add Captain Nemo, but he does not count as a protagonist. Feel free to suggest any others too.

Update 2012-11-22: added Nemo, who cares if he's not a protagonist.