Pick Tone and Finger Tone are incredibly different. The flesh of your fingers gives the attack on the string a darker, fleshier sound while the pick, providing less surface resistance, puts a brighter edge on the sound. Don't let that "edge" mislead you, though, because you can use your fingers to snap the string, too and put a real pop onto the notes you're playing.
The thumb also provides the mack daddy of all flesh tones. You want your strings to sound like they are made of steel cables coated in velvet? Use your thumb. It'll fatten up your tone like nobody's business.
In this lesson we compare pick, fingers and thumb. Combine this with your choices of guitar, effects and amp and the plot thickens!