B/R Hit by throw from F3 to Home

[Manny A]

Alright, first off, you said this was an NCAA game, and all of the subsequent discussion dealt with an ASA rule. The NCAA rule that pertains here when a BR is declared out for interference is:

12.2.13 When she interferes with a fielder attempting to field a batted ball, interferes with a fielder attempting to throw the ball, intentionally interferes with a thrown ball while out of the batter’s box, makes contact with a fair batted ball before reaching first base or interferes with a dropped third strike.
EFFECT—The ball is dead. Each base runner must return to the last base legally touched at the time of the interference. If the interference, in the umpire’s judgment, is an obvious attempt to prevent a double play, the runner being played on also shall be called out.
Note: A batter-runner being hit with a thrown ball does not necessarily constitute interference.

Note the reference to intent in the rule when it comes to thrown balls. As Tom mentioned, you would need to see something pretty blatant that indicates intent by the BR to contact the thrown ball.

NFHS also has the word "intentionally" in its rule on BR interference. For some reason, ASA does not. I don't know if it was intentional for the word "intentionally" to be missing from the ASA rule.