Being 5'9.5", 56cm is well with the "rough" guideline for bike fit. There are many subtle variations that can be done to make the frame fit better. Stem length/angle, saddle set back, handlebar setup are the most common. I would definitely consider asking the bike shop for someone with knowledge to check out your fit and suggest how to fine tune it.

With that said, and as mentioned above, the bike could be a good fit now but you aren't used to it. When I got my first road bike I had difficulty riding much more than 20 miles without neck/shoulder pain. A combination of lots of miles and adjusting my style (I hunched my shoulders too much and had a general "tense" form) helped build me up to centuries with no pain.