Lobbying against environmental or financial regulations is one thing. Taking on the national security state is something else entirely. I don't think it's loony or hyperbolic to say that the military/intelligence world really runs the U.S. at many levels. The U.S. has been a national security state at the highest levels since WWII transformed America from a civilian-centered economy to a military one and created what Eisenhower called the "military industrial complex." The whole topic makes for very interesting history... look into the national security act of 1947 for a starting point.
At lower levels you have a vestigial democracy and true "independent" free enterprise, but when you get to be a company the size of Apple you are too big to blend in with the ordinary civilian economy. Getting that large results in immediate audience before the king, which in America is the military/intelligence shadow state. I'd be very surprised if one can ascend to the billion-dollar stratum in America without some very interesting closed-door meetings with strict NDAs. I'm also sure that all kinds of next-level stuff kicks in when you start to become a major international corporation that does heavy business overseas, as Apple is.
There are endless forms of soft power that can be brought to bear against a large company, especially a publicly traded one. You've got the standard issue tax evasion practices of every major corporation for starters. Don't want to help us spy on users? How about a high-resolution IRS audit and some "offshore banking reform" specifically targeted at you? Then there's anti-trust, which is obviously selectively enforced. Does Apple have anything that could be called a monopoly or a monopolistic business practice?