In the case we are talking about, the companies have to pay taxes but they exploit loopholes to avoid it. They may be not in violation of the letters of the law but they are in violation of the spirit of the law.
The moral obligation is to participate in the funding of the system you are profiting from. Making money by transporting your goods on roads built by the state, employing people educated in schools funded by state, and enforcing your contracts by courts established by the state but not paying taxes towards this system is wrong.
And this obligation does not go away if you find a trick to circumvent the written rules.
You have no moral obligation to pay a tax that is not levied.