> Is it ethical to flag something because the article is related to a company you don't like
I do not think the important topic of Ethics should be brought so low as to help us decide on whether to flag or not a link on HN. Let's replace it by "stupid".
Then yes, it is stupid to flag a post just because it relates to a company we do not like.
However, it is not stupid to dislike Microsoft. You might remember Paul Graham's Microsoft is Dead(1): for people a bit older than 20, Microsoft is a company which was very frightening, a company which did really try to kill Internet, and force all our industry into a nightmarish path where we programmers would all be happy slaves.
Just because they have changed the color of their last make-up will not change this, and I would hope Hackers here and there would actually despise more Microsoft and other similarly dangerous companies.
(1) http://www.paulgraham.com/microsoft.html