The top section of this green-painted Boeing 737's fuselage was slightly faded and I noticed a few dark-green, rectangular patches on its top. They look like patch kits on a bicycle tyre's inner tube. What are they? My understanding is that hairline cracks/weaker spots in the fuselage can't simply be patched like this?
They aren't "repair patches" themselves, they are repainted areas where some sort inspection and/or repair was done to the underlying structure, that required removal of the paint in the area. What the inspection or repairs were done? Well, you'd have to have been there to know, but the 737 does have a lot of structural inspection requirements related to fatigue cracking in fuselage frames and skins.
There may be actually be skin outside doubler patches riveted on in those dark spots to reinforce areas where crack repairs were done, but the borders of the dark spots are just paint masking lines and it's hard to tell in the photo what was done.
Another possibility is that surface corrosion was found at those spots and the paint in the area was stripped, the corrosion was blended out and the zone repainted.
They should probably have their paint guy do some mixing to match the fresh paint to the faded paint, and apply the paint with an edge feathering technique to avoid the sharp masking lines (you have the edges of the mask supported above the surface to allow some paint to spread below, to create a soft edge), so that folks in gate areas looking down at their incoming flights would be less alarmed by the Quilting Bee look.