See generally 49 USC 40116. There are special rules for taxing pay of people engaged in interstate commerce, like pilots. This prevents states from attempting to tax pilot for income earned while flying over the state. Clearly a record-keeping nightmare.

Generally, you're taxed by your state of residence, not where you're based, which is why lots of pilots commute out of tax-free states.

Some states are more aggressive than others in going after pilots based out of state in an attempt to collect taxes. The state of Minnesota is somewhat notorious for going after NWA pilots based out of MSP.

Keep good records, and consult your own attorney/CPA/ whoever for tax advice. I'm just some anonymous guy on a message board.