AFAIK you can, at least in the latest test build prior to release version when you used mouse control only the X and Y axes of the joystick were disabled, the rest weren't so you could freely use your throttle and rudder along with the buttons. Didn't tested it in the release version but I think it stayed that way.
CPU:Athlon64 X2 6000+ MB: GB GA-M56S-S3RAM: Kingston 4GB DDR2 800MHz dualchannel GPU: GB GeForce GTS 450 1GB OC1 OS: Windows XP Pro SP3 Stick: Thrustmaster T-Flight Hotas X Flight Stick Notebook: Acer Aspire 7750G (I5 2430/RadeonHD6850M 1GB/8GB DDR3...
However, I have an integrated HOTAS (both stick and throttle go in one USB). When I activate mouse control I can steer and fire with the mouse but there is no throttle response when moving the throttle. Tried to map mouse wheel as throttle but didn't work.