I'm a developer at Eyeo, working on Adblock Plus. Adblock Plus is not changing Amazon links. TFA is ripe with FUD, but it doesn't even go this far.
Maybe this was a major misunderstanding of the typo correction feature [1], which is opt-in, only implemented in Firefox and merely corrects typos in URLs, always telling what it corrected. I was never really sure how it fits into ABP, but I fail to see how this could be considered shady.
Other than that, the only thing Adblock Plus does is block content. Which content that is depends on the filter lists you use. There are defaults, but you're free to use any you like, or create your own. It's usually ads, but ABP is also pretty good at blocking any kind of tracking [2].
Back to TFA. The main allegations are:
1. The CEO and the angel investor at Eyeo have ties to the ad industry
2. Adblock Plus is letting ads through if sites pay for it
3. Adblock Plus is burning money
One at a time:
1. This is true. Eyeo was founded to find a middle ground between users blocking ads and sites monetising from ads. The idea is that there are decent ads that most people wouldn't want to block, in the sea of horrible ads - "acceptable ads" [3]. "The ad industry" is not a single evil entity that wants to blind us all, some people in it actually want to make ads better. Hence Wladimir joined forces with them.
2. Every site can have their ads whitelisted, and ads that violate the criteria [4] will not be whitelisted. Some sites are supporting us financially, others don't. I think the main controversy is that this feature is opt-out rather than opt-in.
3. I disagree. More than half of the employees on the payroll are working remotely, deliberately. We wouldn't even all fit into the office, which is nice, but cheap (it's a building that's going to be demolished in 1-2 years). We're barely profitable, nobody's getting rich. We manage the infrastructure that delivers the filter lists - which are used by literally every other ad blocker out there, for free, and that's fine. Everything we create is open source [5], everything can be forked, and that's fine.
[1] http://adblockplus.org/blog/typo-correction-feature-in-adblo...
[2] http://adblockplus.org/en/features#tracking
[3] http://adblockplus.org/en/acceptable-ads
[4] http://adblockplus.org/en/acceptable-ads#criteria