I've personally always wondered if animals like elephants or hippos are (financially) worth keeping. I mean, the daily costs are huge. For the same money a zoo could maintain a large collection of smaller or medium sized animals. And what about the costs of building a brand new elephant paddock, or even renovating an enclosure. What about staff time, and don't get me started on space. Is one elephant enclosure worth more than half a zoo filled with smaller animals, even for joe public?
I would imagine it's tricky to weigh the finances of keeping any specific species, but I'm sure many zoos have tried to do so on some level. Elephants, for reasons of space and cost (but also, in some cases, public pressure, and the AZA's new requirements), have been phased out of some North American collections. The two species I would imagine also present zoos with such a quandary are giant pandas and koalas. Koalas, for reasons of diet in many climates (although they are presumably not overly expensive to keep in climates suitable for easy growth of favored Eucalyptus species), and giant pandas because of the financial outlay required by China's loan agreements. Giant pandas, in particular, have led many institutions to publicly (and I'm certain, even more frequently, privately) question the value of housing the species against the cost and other requirements associated thereby.
One thing that can affect the cost to a zoo of exhibiting a certain species is the ease of attracting donors, whether it be single donors with naming rights, donors through capital campaigns, or even animal adoptions. Furthermore, much as conservation of charismatic megafauna can lead to the preservation of entire ecosystems, in zoo terms, I would imagine the inclusion of high-profile species to feature in an exhibit complex can allow the zoo to also integrate less "popular" species while simultaneously improving the educational aspects of the resultant exhibit. For whatever its merits aesthetically or thematically, Elephant Odyssey at San Diego supported the addition of exhibits of some species not previously exhibited at the Zoo and new exhibits for others not previously exhibited. (I, of course, recognize that many other species lost exhibit space, and, as an ungulate fan myself, the loss of the species the once inhabited Horn and Hoof Mesa is still deeply felt). And few, I think, would argue that the gorillas in Congo Gorilla Forest act as a tentpole that helps "support" the exhibitry of the many other species included in that complex. Finally, germane to the discussion here, African Elephant Crossing in Cleveland brought new species to Cleveland's collection (granted, meerkats and naked mole rats are not exactly lacking in representation, but it was nice to see inclusion of a nice collection of new bird species given the relative lack of birds at Cleveland since the all-too-distant closure of the bird house).