I don't think you'll find a record of any particular reasoning unless you ask a designer, but it appears to be mainly another one of those quirky holdovers from ages past. In AD&D, bonus spells from abilities were only given to clerics, not magic-users. Magic-users were the first to get cantrips, introduced in Dragon Magazine #59 in 1982 and Unearthed Arcana in '85. Clerics didn't get orisons until Dragon #108 in 1986 though.
Switching to 2nd Edition, orisons disappeared, and all the cantrips became a single first level spell à la Prestidigitation.
Wizards only got the bonus spells from high Int in 3e. As for why cantrips (and orisons) didn't get the ability bonus when separated back out into individual spells in 3e, there are a few possibly reasons. Most likely is that it was simply an oversight in the cross-over. Wizards got bonus spells from the cleric, the cleric got orisons from the wizard, but the bonus slots didn't appear for 0th-level slots since neither class had had both parts before.
It's also quite possible the designers did not consider them to be worth anything, essentially a little fluff addon from the AD&D era. Having the bonus slots would have also generated extra bookkeeping, since any character with the score necessary to cast spells at all would automatically get at least one extra 0th-level slot at first level, and probably wouldn't care too much about the extra two or three at 20th.