... "if everyone else is doing it, does that make it right?"
From GM's second link:
Official NCAA scorebook and rules
SCORING TERMS
SECTION 2.
v.
Run: The act of an offensive player legally advancing to and touching home plate without being put out.
To answer your question, it's a matter of opinion whether the scoring rules are 'right.' Some would say that a batted ball that results in reaching base should be considered a hit, regardless of whether the fielder missed the ball. Some would say that a pop fly lost in the sun should be rule an error.
Regarding the run scored, I believe that the player who actually scores the run should get credit with the run, for the reasons that Momo'sDad laid out. But there's nothing that says you can't score the way the makes the most sense to those are are looking at the stats.