That is not entirely true Arizona, it depends who you use for construction and the aquarium's location... Marinescape one of the world's oldest aquarium construction companies and will even do feasibility estimates, supply of animals, staff training, etc and their aquariums usually have paid for themselves after 3 or so years...
As to the original question, construction costs, the fact most zoos are society or local government run while most aquariums are "for profit", running costs etc are all factors that increase admission but I believe it is much more complicated than that... The time passed since the first "modern" aquariums (with curved tunnels) were made is coming up to thirty years and people have been very cautious to experiment for fear of upsetting the formula...
Consider the template for the usual public aquarium, it usually sits adjacent to the sea, pumps in seawater and forces it under pressure through filters which makes it quite sterile (lacking the nasties but also strips it of some the natural elements of sea water) and then pumps the water back out to the ocean... This essentially makes the aquarium an extension of the sea and very clean but is very, very energy intensive...
Think of the lighting in all the aquariums you've visited, very little natural light (to protect the water in most cases) and therefore a large air con and heating bill, all this uses heaps of power too...
Think of the building design, very monolithic as it needs to keep out light, support large pumps and of course the heavy weights of water, not very eco-friendly when you think of sustainability design principles (I guess with the exception of the California Acedemy of Science, CAS), acrylic is incredibly expensive, again these types of buildings are very electricity intensive...
Feeding costs as already mentioned can be high, I know when I buy fish from the supermarket..!
So what is the solution to these problems, well quite simply a new type of aquarium design... In Leigh in New Zealand a Marine Biologist started a very small scale aquarium which instead of sucking water from the sea and sanitising it, he filled a set of tanks with sea water in an enclosed system and cycled the water between all the tanks using a bacteria sump and lots of natural light, after trial and error he managed to get the system to replicate all the processes the sea goes through naturally and all the different tanks were inter-relateded, i.e. he had 2 tidal tanks which while one filled the other emptied surging the mud in the bottom of the tank, this feed into different coastal reef tanks, deep sea tanks and finally into a bacteria sump tank with no light whatsoever to deal with the waste... These systems are called temperate eco-system tanks by aquarists...
How is this type of system the answer..? Well firstly you save all the money of large pumps drawing in seawater (buying and operating them), you save all the money of filtering the water, in fact all you need are comparitively small pumps to circle the water... Secondly natural light is not only okay in a system like this, it is needed..! Which means better, sustainable, energy efficient building designs are avaiable, lots of glass, skylights etc all saving on heating costs, with sustainable design like CAS, solar panels etc, basically the only heavy, concrete intensive part of the building would be the tanks themselves... An aquarium like this would use very little electricity compared to a normal one (if you got really serious about solar panels and energy efficiency it could be almost a net zero user of electricity) and be far cheaper to construct, basically tanks surrounded by a facade... Finally this type of enclosed design means the same sized aquarium can support far fewer animals (saving on food costs) which would seem a disadvantage but the plants and environment in the tanks are vitally important to the animals survival and interact with the fish in much more engaging way (i.e. not just fish swimming in a sterile tank) these systems require filter feeders, crusteaceans, coral and plant life, visitors would spend much more time watching as the animals behaved more naturally and in concert with the tank as a whole and the nature of the progression of the water from tank to tank leads itself to a much more engaging "story" as you move through the aquarium...
Of course there are many disadvantages to such a system, one it takes time for the natural processes to start cycling in the tank meaning animals can only be added slowly, the system can "crash" killing the animals and causing the cycling process to start again but all in all I think you would be able to bring the entry price down significantly and provide a much better and longer visitor experience (good for those gift and food shops)... Essentially though it is a far harder and risker system to set up and maintain and this is why I don't think it has been tried on a large scale yet...
Here are some links if your interested, the first is the amazing seafriends ecosystem aquariums:
Aquarium studies
This is Marinescape a pretty fantastic NZ aquarium company:
Marinescape