Why aren't AMA certified radio-control club sites shown on aeronautical charts?
Model aircraft flying areas may be registered with a group such as AMA but there is no requirement to register these areas with the FAA. The current FAA rules expect RC pilots to stay out of airspace in use by manned aircraft, or give way to manned aircraft at all times.
It would require a lot of extra work for the FAA to register every AMA field and mark them all on charts or to enforce restricted areas around them. Also, model aircraft are not limited to AMA fields. This seems to be a reasonable compromise: the FAA lets you use the airspace as long as coordinate with nearby airports and avoid all manned aircraft.
The FAA has provided guidelines for model aircraft flying an an Advisory Circular (AC) as of January 2016:

Model aircraft operators should follow best practices including limiting operations to 400 feet above ground level (AGL).
The aircraft operates in a manner that does not interfere with, and gives way to, any manned aircraft

If you stay under 400 feet as the FAA suggests, you will not be interfering with manned aircraft, which should not fly any lower than 500 feet.
If you choose to fly above 400 feet, it is your responsibility to avoid manned aircraft. You can see them but they probably can't see your model aircraft. Stay aware of your surroundings, use a spotter if you have to.
Remember that the airspace belongs to manned aircraft, and you are only allowed to use it if you don't interfere with them.
See related question: Where is RC aircraft flying allowed in the US?