What an interesting question!

After much thought I can narrow it down to three:

Huckleberry Finn, from Tom Sawyer and The Adventures of Huckleberry Finn. (Also from the Greg Matthews sequel, The Further Adventures of Huckleberry Finn.

Ed Ricketts from Cannery Row, Sweet Thursday and The Log From the Sea of Cortez (real person, but definitely a protagonist)

Toad from The Wind in the Willows by Kenneth Grahame.

Further thought has given me Keith Stewart from Trustee from the Toolroom by Nevil Shute (although many of his heroes are just as memorable)

and His Grace, Sir Samuel Vimes, Duke of Ankh Morpork, Blackboard Monitor and Commander of the City Watch from Terry Pratchett's Discworld.