From the very beginning of the novel, Tolkien characterizes Bilbo as a sympathetic, friendly protagonist. In many ways, Bilbo's shortcomings make him more endearing to the reader. He is not athletic or graceful like the elves or strong as some of the dwarves might be. Bilbo's attributes make him more of an 'every man' that most readers can easily identify with.
Now Bilbo is certainly not without flaws. He is continually fussy throughout the novel, bemoaning the loss of his handkerchiefs, comforts, and extra meals. The reader, however, overlooks most of Bilbo's personality quirks in favor of his deeper virtues--his perseverance, loyalty, and clever mind.