Toads were amphibious in D&D 3.5, but that doesn't seem to have carried over to Pathfinder. Frogs and toads are amphibians in the real world (most species can breathe in both water and air indefinitely). Have the designers said why frogs, toads, and their giant variations aren't amphibious in Pathfinder?
Since frogs and toads cannot breathe water, they don't match the aquatic subtype description and should not be amphibious.
From the Universal Moster Rules :
Creatures with this special quality have the aquatic subtype, but they can survive indefinitely on land.
Format: amphibious; Location: SQ.
From Creature Types and Subtypes :
These creatures always have swim speeds and can move in water without making Swim checks. An aquatic creature can breathe water. It cannot breathe air unless it has the amphibious special quality. Aquatic creatures always treat Swim as a class skill.
Some changes made in Pathfinder are here mainly to reduce the amount of text to work with, then every creature type and subtype has a very clear and unambiguous description.