I'm about to take a position with a certain group that hasn't been getting very good press about their computer security. Even if my job doesn't really pertain to that sort of work, am I still in danger of my resume being thrown in the trash for being associated with them?
I doubt it.
Most people in technology recognize that major security problems are usually caused by bad strategic decisions by executives and managers, or isolated screw-ups by individual developers, or a combination thereof. So we don't hold everybody who works for such a company responsible for those problems.
For instance, Google's been in a lot of hot water lately over drive-by snooping and data retention from peoples' wi-fi networks. There's been lots of discussion of whether that was really (as Google publicly claimed) an individual developer accidentally leaving in some debugging code, and if so, whether the folks in the chain-of-command above that developer were derelict in their responsibility.
But I can't imagine somebody from a different part of Google applying for a job elsewhere, and being rejected because they have "drive-by data collection cooties".
Not at all
For example; if you are an accountant at Sony and we all know what happened there... How are you to blame?