SmuggleNutz
Explorer
I don't like it. Using spells (or magic items) to fly does not give you flight as a class skill, and hence the +3 bonus. All it does is let you start putting ranks into the fly skill from that point onwards.
Only creatures with actual fly speeds in their basic racial stat block (they have wings to fly or their race has some kind of innate magic flight power that is always active) get this "flight is treated as a class skill" perk.
Well, that came up here too, and that argument is not supported anywhere in the rules. The line "creatures with a fly speed" is written broadly, but it is what it is. Plus, it just makes sense that creatures able to fly would gain a benefit from being able to do that, especially if they actually do it every day.