No, you are not flat-footed. You are only flat-footed if you have not yet acted in combat, and acting on the surprise round means you've already acted in this combat encounter and are not flat-footed.
The only time you would be still flatfooted after a surprise round is if you were the one surprised, and then I the next round you still have not acted in order of initiative.
Otherwise it would take someone actively using an ability on you to make you flatfooted