Why is my low pass filter attenuating everything so much?
The filter pulls your signal source on its knees. Try about 100x bigger R1 and drop the capacitance of C1 to about 0,5uF. 

To be exact the output impedance of your signal source and the input impedance of your amp should both be taken into the account. Unfortunately I do not know them.

BTW 1st degree RC-lowpass filter has poor frequency selectivity. The attenuation increases as the frequency increases but there's no clearly noticeable steep frequency limit. 2nd order filter would be much more selective.