The Constitution requires states to ensure equal protection of the law. That means nobody gets special exemptions because of who they are or any quid-pro-quo they may offer.
I understand where you are coming from and why corporate welfare bothers you (corporate welfare bothers me too) but if you think about this particular case in a different way I believe you'll see why this doesn't fit the bill for a case of corporate welfare or have any applicability for equal protection (or Article I section 8 Commerce).
This transaction represents a State Government EXPENDITURE, just like any of the other expenditures that State Governments make, like for example building a road. If the State wants to build a road, it'll follow whatever bidding process is prescribed by it's State Constitution and it's legislative process and award the contract to
some company to build it, all of
some companies competitors don't have an equal protections case because they didn't win the bid do they? They don't have any commerce clause recourse do they? The only legal recourse they would have is if they could demonstrate the process was rigged, right?
The same case here, Apple put this proposal out for "bid" to some amount of States and the State Government of Iowa decided (based on some criteria) that it was in the best interest of the State to buy it and offered a bid to Apple, this didn't mean that any other company couldn't offer up similar proposals to the State of Iowa, just means Apple offered up the (in the opinions of the Government decision makers) the best deal for the money spent.