How can I get paint on rocks to last longer?
Strength of paint bonding depends on the surface.  A surface with lots of microscopic roughness, like something worked over with 400 grit sandpaper, is going to bond well.  Something microscopically smooth, like a sheet of glass, will bond poorly.  But even on a poor bond, the paint will want to stay there just for lack of physical motiviation to go somewhere else.  

Weather is not enough to provide that motivation.  It needs help, with a stripper that is compatible with the protective layer, and/or scrub brushes and elbow grease.  This is a hard problem, and transit agencies with rail operations are at the leading edge of the field.  (Building managers less so, since they can repaint.)  They use rather exotic paints you will not find at Lowes.  This may be a lot of work. 

Hydrophobic films can only work against water based paints.   Common graffiti paint in spray-cans is oil based.    In any case, hydrophobic coatings are not magic, they can't make the applied paint levitate and move downrange.  The paint will still sit on the protected item, will just hopefully be easier to remove.