Companies don't exist in a vacuum, as evident in that very few companies prefer to put their offices in the middle of the sea or deep the jungle. They benefit greatly from infrastructure of our society, and it's fair that they should pay their share to build and maintain it.
Companies playing legal games around taxes is exactly the behavior that the complicated tax code incentivizes. Play games, get money. Are corporations not supposed to play? It's parallel to programming productivity measurements. If a company starts counting LOC and rewarding it, they are going to get precisely what they asked for: More lines of code.
There are a lot of people who think that much (if not most) tax dollars go to waste, so they do not want to pay because they think that taxes are funding harms to their fellow citizens and foreigners. I am one of those people, and I do not want to be responsible for hurting my fellow man.
I wonder if you would be so principled if it cost you money rather than saved you money.
I use the roads which I (and all my fellow citizens) are forced to pay for, at least partly because the government has crowded out all the alternatives. With respect to firefighters, I would be very happy to return to the system where the insurance company provided fire-fighting services, as was the case before the government took over the industry.
I have often made the case against policies that greatly benefit me (financially and otherwise), but at an unacceptable cost to others, and I am sure that I am not alone in having done so.