It clouds the discussion on neutral issues and fair analysis when people are emotionally or otherwise invested in companies.
For example, see HN comments on news/opinion involving patents, Google, Android and Apple. They devolve in flamefests because people think that their particular company is being wronged, regardless of their original stance on patents etc. before such news involving their companies came out.
Asymco's analysis always seems to make errors that favor Apple, like leaving out HTC from stats on how profitable Android OEMs are. Or something like this http://news.ycombinator.com/item?id=2887430
Same with Gruber with his extreme pro-Apple spin on everything. Or Marco's 'analysis' http://news.ycombinator.com/item?id=2878329
It's very telling how some geeks find Gruber, Asymco, Marco etc. very insightful, whereas others find them inane and biased to a fault. No wonder the discussion runs into a flamefest with very harsh moderation.
Not singling out Apple here, there are examples where criticizing Google will get you automatically downvoted here on HN.
Some part of the moderation seems to be on 'party lines'. Criticize Apple or Google, or support MS and face downvotes or no votes. Criticize MS, get a boatload of karma. All this regardless of the actual facts on hand.
As you say, all this may be good for companies, especially ones that carefully cultivate their brand image to use such effects positively, but this is not really beneficial to honest discussion, information or analysis. It turns the conversation into Fox News vs. MSNBC. with people unable to admit their favorite company can do something wrong once in a while, resulting in people mudslinging the competition instead.
Also, see Roughly Drafted and Boycott Novell(now techrights.org).