Fillets won't help you with that problem. Additionally, fillets are almost always a structural item. Any aerodynamic benefits they have are secondary to their main purpose of making sure your fins stay on the vehicle in flight.
Rail speeds are slow enough that drag will not affect them at all. The difference in drag force at such low speeds is essentially negligible compared to the gravitational force on the rocket.
There are 3 ways you can increase rail exit speed:
1. Decrease rocket mass, thus increasing acceleration and rail exit velocity.
2. Change to a higher thrust motor, thus increasing acceleration and rail exit velocity.
3. Increase the length of the rail, thereby increasing the distance over which you can accelerate.
That's it. You can choose between accelerating faster and increasing acceleration distance. There are no other ways.