Please forgive me if some of the comments are too obvious, but I'd mention them just in case:
Do you see the clock waveform for the input clock signal? If you don't, then something is very wrong and focus on getting the clock waveform before anything else. Note that you must perform the "clock" command on
every single simulation run, each time you restart simulation. Also make sure you are not "zooming" too much (yeah, too obvious, but it happened to me a couple of times).
Check if you don't have a global async reset that is resetting all the flip-flops.
Check for implicit power-up register values. FPGA registers power-up to zero by default. Quartus simulator (I believe) is aware about that, but ModelSim doesn't. Unlikely that this is the problem, because if so you would probably get X (unknown) as your outputs, and not zero.
Are you using/simulating a PLL? If so, then simulation time units must be 1ps.