Aside from bus line 56, which goes to and from Zeist, the best (and almost only) way to get to and from Soesterberg is by bus, line 52, which runs from Amersfoort to Utrecht and back and goes through Soesterberg in three stops.
Pricing is simply by the national Strippenkaart, which can be bought at any railway station, post office and most supermarkets.
The National Airforce Museum in Soesterberg is quite easy to be found. Follow from Amersfoort the freeway to Utrecht or vice versa and take the exit "Soesterberg". At the end of the off-ramp there is a sign clearly pointing you in the direction of the "Militair Luchtvaart Museum". There's enough parkingspace, so no worry where to leave the car, but ... wouldn;t it be nice to visit it arriving by airplane?