Let me make a wild guess. You use the /Q output of the 555 which normally stay high and pulse low. So it goes from +5V to 0V when triggered and stay for a short time and goes back high again until the next trigger.
With the RC filter, you see the output normally stay close to 0V, then the pulse goes to -5V and come back to 0V. Am I right so far?
If so. It is a duty cycle effect since you have a capacitor to block the DC. The reason you see the output goes from about 0V to -5V is because at the rest condition, the output is at 0V. But when you pulse low, the output goes from 0V to -5V due to the AC couple. Any signal that is AC coupled, the average of the signal has to be 0V. Because output at the 555 only goes low for a very short period of time, the output after the cap sit mostly at 0V. From the scope picture, your duty cycle is only about 20%( 20% low and 80% high). With AC couple, the average has to be at about 0V. With 80% high and 20% low, the voltage at the output should be +1V to -4V. Double check you scope again, find the 0V level, it cannot be from 0V to -5V. Double check and you'll find it is from +1V to -4V if it is 20% duty cycle.
But you should get what I am trying to say. Because of the duty cycle, the AC signal seems to cocked to the negative side. If you have a square wave at 50% duty cycle, you'll see it goes from +2.5V to -2.5V after the cap.