The effect you noticed is a function of strength and size.
When you have a large window, and a sonic boom comes along, a relatively small pressure difference can set up very large tensile forces in the surface of the glass (especially if the shock wave cannot easily "go around the back" of the glass). When there is a bending stress, all you need is a small (surface) crack to act as a stress concentrator and you will get crack initiation: and once the crack is initiated, it will propagate as long as the stress is maintained*).
This very simplistic answer shows there are several differences between windows and humans:
- size: the human is small relative to the wavelength of the boom: this means there will be less opportunity to build up stress, as pressure is "all around"
- elasticity: when you are hit with a shock wave, your lungs will collapse very slightly (your chest compresses) but that doesn't hurt anything; by contrast, the glass tries to resist the motion and builds up stress
- compressibility: you are mostly made of water, which is highly incompressible. A sonic wave will hardly compress anything made of water - but it can deflect glass when there is just air behind it.
The notable exception to all the above is the ear: there is an enclosed air pocket behind your ear drums, and the ear drum will move violently back as the shock wave hits. This can do permanent damage to the structure of the ear, including rupture of the ear drum.
When people go scuba diving, they can be subjected to pressures that is many times greater than atmospheric pressure - yet they survive. It's not the pressure that kills, but the pressure difference. Humans "equalize" quickly - ears and sinuses are possible exceptions. Incidentally, when divers try to surface quickly, they have to make sure to breathe out continuously or they will rupture their lungs (as a pressure difference would build up between lungs and surroundings).
None of the above is meant to imply that it is not possible to create a shock wave that can damage human tissue; but the combination of compliance, size and toughness means that a glass pane will shatter rather easily compared to more diffuse damage in human tissue (at sufficiently high pressure levels).
*) Specifically, the fact that the glass will first bend and store elastic energy means that once the critical stress is reached (which is a function of surface condition and possible built-in stresses) a lot of energy is available / released quickly, resulting in acceleration and branching of the cracks and (frequently) complete disintegration. For some glass, this is a deliberate effect: during manufacturing the glass is tempered in such a way that internal tension is built up and the outer surface is under compression. This raises the threshold before cracks will initiate (for that, the surface has to be in tension); but once it reaches that threshold, the crack, propagating into the center of the glass, encounters material that is already in tension. This makes the crack accelerate and bifurcate. The result is that the glass breaks "completely". You are less likely to be hurt by many small pieces of glass than a single big one, because the small pieces will have less momentum.