Google Penalizing for Some Non-Paid Links

[Yinka]

On Google Webmaster Help a guy website was penalized and he was trying to understand why. JohnMu a Google employee chimed in to explain why this guy website was penalized, here's part of what JohnMu said

I browsed your site's reviews a bit and most of the links are either affiliate links or links to the companies without nofollow.

What was interesting was the last part, "links to the companies without nofollow". I take it that a website can be penalized if they have a regular link on the same page as an affiliate link if they share the same domain name.

Basically, if I had an article and let's say in the first paragraph I named the company name and gave the URL to the homepage (without nofollow) --- this is not an affiliate link and no one is being paid for this link then in the last paragraph I gave an affiliate "paid" link to that same company product page (with nofollow). The meaning I am getting from JohnMu comment is that the link to the company homepage (without nofollow) can still get your website penalized, just because of its affiliate association --- even though the affiliate link is nofollow and not passing any juice. It doesn't matter the homepage link is a regular, non-affiliate and non-paid link. Does this make sense? Or seem logical? Anyone know of this happening elsewhere?

Source: [google.com...]

[tedster]

The comment from JohnMu is a bit difficult for me to push into a generalized understanding. It seems that the site in question had an imbalance of too many followed links that still looked like there was a financial arrangement. Hard to tell now, since the guy has made a lot of changes.

It does seem like JohnMu was pointing to a paid link detection factor, since it's clearly not a thin affiliate/boilerplate text kind of site. I also noticed this comment from the site owner with some interest: "Manufactures send me products to review."

[Robert Charlton]

The above JohnMu comment is taken out of context. There was a line of discussion with another poster, before the exchange with JohnMu, suggesting that the original poster's interlinked niche domains, all in the same market area, might well have looked like a domain farm to Google.

The OP, responding to a question about whether he was selling links, had replied...

I only sell nofollow links

John Mu responded (my emphasis bolded)...

I browsed your site's reviews a bit and most of the links are either affiliate links or links to the companies without nofollow. This doesn't seem to match your reply regarding the use of nofollow. Perhaps it would be good to double-check and submit a reconsideration request should you find something that could be improved.

The meaning I'm getting from JohnMu is that it's likely that Google would have tagged the sites as a domain farm that were selling links with or without the affiliate links, not because of the affiliate links.