2005 Chevy Cavalier Idling rough, as if to stall

I just recently change my fuel filter on my 2005 chevy cavalier, now it hesitates when i accelerate and when i turn on the air hot or cold it runs rough, when i going down that freeway it seems to run fine. when im trying to accelerate quickly the check engine light flashes quickly and sometimes stays on. Eventually it goes off, depending on the weather, it lags eats a lot of gas finally picking up speed.