This is just an opinion, but seeing the bonuses in original D&D (OD&D) since the beginning, they seem to be a way to subtly push the player towards a specific character class. Remember, in the early days, many systems (including OD&D) required you to roll three dice, in order, for your stats. So many players who wanted to work a fighter might end up with a 9 strength and a 17 wisdom, and they would just play the fighter despite having bonuses should they have played the cleric. It appears the prime requisite bonuses might be there to reward a player for "taking a chance" on a character class he might not normally choose. The 5-10 percent added to experience (in contrast to the 10-20 percent LOST if the prime requisite was 8 or under) would be a substantial bonus in early editions of the game where EXP were sometimes scarce and character longevity was not guaranteed.
EDIT: BTW, per a question by Yogo, here is the original Prime Requisite bonuses from the OD&D rules. It is interesting to note the changes from this to later editions:
In OD&D there are only three classes: Fighting Men, Magic Users, Clerics.
All abilities are rolled by 3d6, in order.
STR is prime requisite for Fighting-Men.
INT is prime requisite for Magic Users.
WIS is the prime requisite for Clerics.
Bonuses and Penalties for Advancement Due to Abilities:
Low score is under 8; Average is 9-12; High is over 13
Prime Requisite 15 or more: Add 10% to earned Experience
Prime Requisite 13 or 14: Add 5% to earned Experience
Prime Requisite 7 or 8: Minus 10% from earned Experience
Prime Requisite 6 or less: Minus 20% from earned experience
There are ability bonuses given for high CON, DEX or CHR, but they are unrelated to Experience point awards. Interestingly, besides the Experience point bonuses there is little advantage to having a high STR, INT or WIS except for intangibles: A high STR is said to help in opening traps, A high INT will add languages and affect referees decisions about certain actions the player might make, A high WIS acts in the same way as a high INT (might affect decisions made per the referee's decision)