RC circuit understandings
The key is the RC time constant. This is the product of the resistance and capacitance in series. For your example, that would be 3,300 ohms * 0.0000001 farads, which results in 0.00033 seconds. In order for the capacitor to fully charge or discharge, you need to wait for 5 time constants. In your example, the capacitor will reach only about 75% of full charge / discharge during the half period of the 1 kHz square wave. Consider decreasing your frequency, or using a smaller capacitor or resistor.

Other possible issues can include:


Incorrectly connecting the circuit. The capacitor, resistor, and function generator should all be in series.
Using the wrong tool for measuring the voltage. For the results you are expecting, you need an oscilloscope. A multimeter won't give you the same results unless your time constant is near a second in magnitude.
The pattern generator has a high output impedance. This is unlikely, but if the impedance is close to your resistor value, that will throw off your calculations.