There are three components of this site: 1) the Ismaili Centre, which is not just a religious entity, but also a community centre available to the community at large; 2) the Aga Khan Museum, which is a cultural institution in the same way as the AGO and ROM, both of which, by the way, receive funding from the province and, in the case of AGO, from the city; as they both also have charitable status, I would argue, so should the AKM and IC site; 3) the surrounding park, which is freely open to the public at any time. Each of these supports the request that the site should be tax exempt.
This is not a commercial venture for profit. Everything built here is for the benefit of the people of Toronto, Ontario and Canada. What's more, except for some supporting infrastructure, these were all built without any contribution other than from the Aga Khan. Asking for taxes to be paid would a slap in the face.