I think we have to question the benefit of spending taxpayer money to subsidize a private company. Thats effectively what we're talking about. And thats fine, as long as we get something in return.
The Toronto Port Authority is a public body, not a private company.
Neither the TPA nor their principal airport tenant, Porter Airlines, particularly "benefits" from an investment in access infrastructure. It is the users of the airport and the customers of Porter Airlines that benefit. Porter Airlines can operate pretty much the same whether the tunnel is built or not.
If building a tunnel leads to more people flying Porter, then Porter could be considered to have benefitted (and the Port Authority will benefit from more airport fees), but it is those people using the tunnel that benefit the most, no longer having to wait for the overcrowded ferry.
If the building of a tunnel leads to fewer ferry trips across the channel, then the neighbouring community will benefit as well (even beyond having even easier access to regional air travel).
Personally, I don't think the idea of "stimulus spending" is a very good one, but if the federal government is going to throw money and various projects across the country, this project appeals to me a lot more than most of the ones on the list.
While I would prefer the government to simply not spend the money (and maybe reduce taxes), that option doesn't seem to be on the table. At least the tunnel can be expected to benefit tens of thousands, if not hundreds of thousands, of Canadians.
EDIT: In a similar way, I support the expansion of the subway platform at Union Station even though that "benefits" one company (the TTC) since it is actually the subway passengers that benefit from having a less crowded platform.