In the "great rift" that has divided many atheists over the years, guilt by association generally referred to negatively evaluating someone on the basis of who they associate with and/or promote. For example, a blogger who promoted the work of Sam Harris might be judged as "gross and racist" for doing so. Whatever faults Sam was perceived to have must apply to this blogger because otherwise he or she could not possibly value anything Sam had to say. This sort of guilt by association involved condemning someone who chose to associate with persons who critics considered "problematic."
As irrational and counter to freethought as this sort of thing was, it could have been much worse. At least with this type of guilt by association, the condemned was being negatively evaluated on the basis of a choice he or she had made (i.e., the choice to associate with or promote someone who Scientologists might label a "suppressive person"). This was part of what led those issuing the condemnation to feel it was justified. They were condemning someone for something that person had done, something they regarded as a bad decision.
There is a different type of guilt by association, though, and it is one that is much less rational, far harder to justify, and more toxic. This other type of guilt by association has nothing whatsoever to do with any decisions someone makes or any actions he or she has taken. It involves condemning someone for the actions of others, actions over which the condemned has no control. In fact, the condemned does not even typically know what is happening until it is far too late.
This sounds vague, so we need an example. Suppose that a blogger writes a post critical of Islam in which she highlights the perils of women living in a predominately Muslim country like Saudi Arabia. Now suppose that a member of a thoroughly vile far-right group (i.e., a group that is genuinely bigoted against Muslims) finds her post, decides that a portion of it would serve to advance their cause, and begins to promote it. Perhaps it is shared on this group's social media channels where other members of the group "like" or retweet it. This second type of guilt by association occurs when others decide to condemn our blogger because members of this far-right group like her and have promoted her work. They are bad people, so anything they like must be bad.
Granted, some of those seeking to condemn our blogger may recognize that condemning someone because someone else likes their work is more than a little unfair. But instead of backing off, they seek evidence to support their condemnation. They'll go through every word the blogger has written to find anything they can use against her. And if they can't find much, some will go so far as to distort what they find to justify their condemnation. They will accuse her of saying things she never said and twist her words into whatever they need her to have said in order to feel justified in their condemnation.
I realize that the problem with hypothetical examples like this is that they may sound unrealistic. Here's a concrete example of the sort of guilt by association I am describing here in the form of an unfortunate piece written by Stephen Ledrew at Religion Dispatches. Essentially, Sam Harris is condemned for a combination of the distortions Ledrew engages (Sam has rebutted these distortions repeatedly on The Rubin Report) and because some of the dreaded "alt-right" has supported some of what Sam has said. Ledrew gives Richard Dawkins the same treatment. His argument boils down to this: these men are bad because some bad people like them.
This is a particularly toxic form of guilt by association. Harris and Dawkins are responsible for their own words and deeds; they are not responsible for who likes them. The same is true for you or I. The notion of condemning someone on the basis of who likes them is about as irrational and tribalistic as it gets. As freethinkers, we can do better.