Our value is keeping the catalog up-to-date and putting a nice interface around the updating process. Not ad-blocking.
We actively uncheck toolbars for maybe 5 apps. If those apps removed their toolbar offers people would still use Ninite to track updates and automate work.
On profits XOR good: We do make money, but we also work really hard to do good as in http://www.paulgraham.com/good.html
Our website is completely free (and ad-free) for home users. We save people from about 15 minutes of mindless installer work every second.
Our $9.99 home Updater product is just something to point home users at when they ask to donate to us. We're a company. We don't take donations.
We also run http://ninite.com/accessible to help visually-impaired people manage software. Actually, until last summer that was about the only way for people to install Flash with a screenreader http://blogs.adobe.com/accessibility/2012/07/flash-player-in...
If publishers want to make updating their software artificially hard there's not a lot we can do except trust that people will see what's going on and move to other products.