Simulating AC-Coupling capacitor used in PCIexpress
If you look carefully at the graph, you will see that the average voltage after the coupling capacitor is slowly drifting down -- at first the bottom is 0.0V and the top is 1.0V, but after the 4th pulse the bottom is almost -0.1V and the top is almost 0.9V.

I expect that if you run a longer simulation with 100 pulses, the average level will become 0V as you were expecting.

You can calculate the time constant based on your component values as $$\tau = RC = (100\:\Omega)(1\times10^{-10} \text{ F}) = 10\text{ ns}$$

It will take a few times longer, or about 30 ns, to settle.