If something is bad, then it's bad even when it's done by your team.
The end does not justify the means.
Lobbying is berated because economic organizations should not be granted larger influence on governmental officials than the people en mass in a democratic republic, and most people would argue that is the current state in the US.
Once a company invests in lobbying, lobbyists have an incentive to keep clients on retainer, so they look for rent-seeking opportunities that they can justify on an ROI basis. Hence all the shenanigans around taxes. Spending $500k on a lobbyist to save $1 million in taxes is a no-brainer.
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.
But "Lobbying", the practice, is understood by the public to be the process whereby monied interests essentially buy votes via graft, bribery, etc and/or buy votes via contributions to re-election campaigns.
The result being that it is (usally) not the speech and thus the data or moral argument that changes minds in government, but the money.
And that is what's inherently bad.
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)