In the past when we have flown, we had better luck telling the check
in reprensentative when we arrived at the airport and/or the flight
attendents at the gate and on the plane. They were always more
accomodating ( if only to give us a peanut free zone in our section)
We also always board the plane first and wipe everything we think our
son would touch with clorox wipes and cover his seat with a bed sheet
from home. We also brought one of those disposable placemats to stick
onto the flip down tray.
And of course bring his own snack :)
Hope this helps you
Melissa