If a federal law is written such that every person in the US is to receive a payment of $100 and the administrators withhold subsidies from some persons there would be a due process issue.
If a state law is written such that every person in that state is to receive a payment of $100 and the administrators withhold payment from some persons there would be a equal protection issue.
In either of these scenarios the process of law was not followed, was not applied equally.
Neither of these scenarios occur with PPACA subsidies. That federal law unambiguously specifies subsidies are available to those who purchase insurance through “an Exchange established by the State”
Laws make distinctions between persons all the time, but they must be reasonable distinctions.
A law that distinguishes persons based on skin color is unreasonable. A law that distinguishes persons based on some ability is reasonable, for example not everyone may lawfully perform eye surgery.
But the law must be equally applied. An eye surgeon can not be prohibited from performing surgery simply because of his politics. Similarly, the IRS can not interfere with a tax-exempt organization simply because of their politics.