The association bonus FAQ says:
This bonus gives users who have shown some basic understanding of how the Stack Exchange system works a boost past the initial site restrictions on sites where they have low reputation.
And it lists privileges (up-vote, comment, flag, etc.) about which it says:
You can lose the bonus reputation on a single site through the normal means: giving it away in bounties, downvoting answers, getting downvoted, having a post deleted as spam or abusive, etc.
However, once you earn the association bonus rights, you can't lose them.
(Bold added, but italics as shown)
Now consider this user ‡ (not me).
He's a good citizen on 120 sites, well versed in responsible up-voting, commenting, flagging, etc. Yet, because he offered a bounty on one site, he can no longer upvote helpful posts, nor even flag spam, on that site.
Now some might say that he should just knuckle down and answer questions, or something, until he gets back to 100 rep, but not everyone has the time or the inclination to post something useful on all of the 100's of sites where they otherwise help out.
(Personally, I've flagged spam and upvoted on about 150 sites, but only posted on about 27.)
That defeats the purpose of the association bonus, and why should the exceptional, literally Altruist be penalized so?
Further, even if a user lost the reputation by less honorable means, that almost never means that they can't upvote or flag correctly. (And we have other ways of dealing with the relatively rare cases of abuse.)
As the FAQ states, The base, know-how-to-work the site privileges, provided by the association bonus, should stick -- even if the user's reputation drops due to giving bounties.
‡ The user is not me, but rather asked a question that lead me to this bug. But I tested it myself and verified that the association bonus privileges do not stick.