That is, all this "good" lobbying was by organizations operating on behalf of a large group of individuals who don't have the same shared profit-driven interest.
So profit = evil is the crux of the argument? The Chamber of Commerce is a non-profit while many Sierra Club sponsors are businesses who benefit from the regulation they promote.
When people or organizations get together and lobby the government so that their business or industry makes more money as a consequence of the changes they're lobbying for, then yes, that's bad. Sure, corporations should be able to influence policy, but this influence must happen democratically and out in the open, and potentially opposing parties must have an opportunity to comment.
The fix doesn't lie, however, in hoping that businesses will voluntarily stop lobbying, so I won't criticize back-country tourism companies from giving money to the Sierra Club to ensure that their venues remain unspoilt. Even if a business didn't want to, it might nonetheless feel compelled to lobby congress for reasons of competitive advantage. When many entities feel compelled to act in opposition to their ethics, it's a sure sign that the system they operate in is broken.
(That said, many businesses sponsor the Sierra Club for P.R. reasons, which is fine and categorically different from the "bad lobbying" explained above)
Corporations are not just businesses. They are the way that people with a common interest can pool their resources to coordinate on a common goal.