Rows allow you to lift more weight, and are therefore the superior option for building muscle strength. However, flys are an isolation exercise that may offer better focused muscle stimulation, and hence overall muscle gains too.
You can typically train with heavier loads in a rear row than a backwards fly because the load (Weight used) is closer to the point of effort (Shoulder muscles). Therefore, you have more of a mechanical advantage. Whereas with a fly, having extended arms creates a longer lever which requires more effort since the load is further away from the pivot point or the joint.
Both are very excellent movements to incorporate in your shoulder training routine.