Mostly correct, except it's only indirectly the surface of the "atom" - because of the way covalent bonding works, there's continuous electron density between atoms too. It's just that the region around the nucleus is the most electron-dense. And yes, those look like phenylalanine or tyrosine (amino acid) sidechains to me, both of which have a benzene ring at the core.
(For the record, there is also something called neutron crystallography, which works like X-ray crystallography except it's the nuclei that diffract, not the electron clouds - which allows you to visualize hydrogen atoms more directly, and even resolve the difference between hydrogen and deuterium. But it's another speciality technique, in part because neutron sources are so much weaker.)
EDIT: since I actually did some work on visualizing electron density maps on the web, here's an interactive view of an older X-ray structure (from 2003, at only 3Å resolution) that shows how a protein molecule fits into the density:
http://natechols.github.io/xtal.js/map_viewer.html
(click and hold the middle mouse button to pan through the molecule)
(For the record, there is also something called neutron crystallography, which works like X-ray crystallography except it's the nuclei that diffract, not the electron clouds - which allows you to visualize hydrogen atoms more directly, and even resolve the difference between hydrogen and deuterium. But it's another speciality technique, in part because neutron sources are so much weaker.)
EDIT: since I actually did some work on visualizing electron density maps on the web, here's an interactive view of an older X-ray structure (from 2003, at only 3Å resolution) that shows how a protein molecule fits into the density: http://natechols.github.io/xtal.js/map_viewer.html (click and hold the middle mouse button to pan through the molecule)