It is a reality that emergency room personnel must be on the look out for child abuse. As you say, one of these signs could be frequent visits because of injuries.
Unfortunately, it does happen from time to time that a red flag is raised and parents are put under suspicion when they may be innocent. However, for the most part, the doctors and nurses are able to look at the situation and draw conclusions from the actual injury. Certain types of fractures in certain age children, for example, are a strong indicator for abuse because of the way the bones are broken.
If you and your child are open with the staff and are able to explain the injuries, it isn’t likely that they will think you are hurting him.