On balance I agree with Chris, due to the risk of a merchant being misrepresented.
E.g. Merchant sells grey widgets. That's all they sell. Affiliate bids on 'white widgets' as it only costs 2p a click and might convert despite the fact that the merchant only sells grey widgets. Customer clicks through to merchant's site, can't find white widgets, and blames the merchant for misleading advertising. Merchant ends up getting a bad reputation. Not all traffic is desirable, even if it is free.
I comepletly understand the problem of ppc vs
seo with regard to this issue, and no doubt this will be addressed in time by some merchants too.
I'm not saying I like it, but I can see where merchants with these policies are likely to be coming from. Some merchants will of course misuse negative keyword policies, and I think this is possibly Shane's concern, but if we don't like it we don't have to promote them.