Lots of the answers so far have focused on the economic reasons why a floating city is impossible. But what about physical reasons?
Aerodynamic Levitation
As a first approximation, we can treat the city as an air bearing. There are a couple formulas that we can take from an intro fluid flow class to calculate the amount of airflow required to hold us up, assuming incompressible laminar flow.
$$
\dot M \approx \frac{\pi b^3 \rho\sigma g}{3\mu}
$$
Where $b$ is the distance in between our city and the ground, $\rho$ is air density and $\mu$ is viscosity, $\sigma$ is the load of our city and $g$ is gravity. Here are the values I assume:
- $g = 9.8~\text{m}/\text{s}^2$ (Earth standard gravity)
- $\rho = 1.225~\text{kg}/\text{m}^3$ and $\mu = 1.789\cdot 10^{-5}~\text{Pa}\cdot\text{s}$ (standard air at sea level)
- $\sigma = 1000~\text{kg}/\text{m}^2$ Assuming the average density of stuff (buildings, dirt, etc.) in the city is around the same as water, and if you flattened the city out it would be a meter high (this is a huge underestimate)
- $b = 1000~\text{ft}$ This is what my intuition tells me is a "reasonable" height, something like the spaceship in District 9.
We can plug in these values and we get:
$$
\dot M\approx 1.5\cdot 10^{15}~\text{t}/\text{s}
$$
Yes, we need to move over a million billion tons of air per second to keep the city afloat, or enough to turn over the whole atmosphere in around three seconds. Now, this is obviously not going to be laminar flow anymore; we can calculate the air velocity at the edge of the city, assuming a diameter of $2R=45~\text{km}$:
$$
v = \frac{b^2\sigma g}{\mu R} = 20\cdot 10^{6}~\text{km}/\text{s}
$$
This is obviously wrong, since it's 60 times greater than the speed of light. However, it does tell us that we can't levitate the city this way.
We can try another approximation, this time using actuator disk theory. It tells us that the amount of power required for the city to hover is given by:
$$
P \approx A\sqrt{\frac{\left(\sigma g\right)^3}{2\rho}}
$$
Using the same values as before, we come up with a power of:
$$
P \approx 1000~\text{TW}
$$
... which is 50 to 100 times current global energy consumption.
Even if we could circumvent these issues, we'd still have to apply a couple of psi to the ground below to support the weight of the city. This would certainly flatten any fields that city flies over, and if the force is applied in even a slightly unstructured way, this could easily flatten buildings. In addition, the ground itself could give way when you fly over another city: imagine doubling the weight of every building, and the settling that would occur.
Hydrostatic Levitation
We can get around the ground pressure problems by replacing the weight of the air that's already there; that is, floating the city with balloons. As a best-case scenario, I'll assume that the balloons are filled with vacuum.
To see how this works, imagine cutting out a disk-shaped slab of air and replacing it with a rigid shell. If the total weight of the shell is equal to the weight of the air removed, the forces on the surrounding air will be exactly the same, and the people on the ground won't feel any pressure.
I'll use the same figures as before for our calculation: a base height of $1000~\text{ft}$ and an average mass of $1000~\text{kg}/\text{m}^2$ (around $1.4~\text{psi}$, or $0.1~\text{atm}$). We can set up the following equation relating the mass of a section of the city and the mass of the air it displaces:
$$
m = \int \rho\ dV \\
\sigma A = \int \rho\ dz\ dA \\
\sigma = \int_{b}^{b+\Delta z}\rho\ dz
$$
Using the US standard atmosphere, I get a value $\Delta z = 2900~\text{ft}$. If we using a lifting gas with density relative to air $\tilde\rho$, the equation becomes:
$$
\sigma = (1-\tilde\rho)\int_{b}^{b+\Delta z}\rho\ dz
$$
For helium with $\tilde\rho=14~\%$, we get $\Delta z = 3400~\text{ft}$. Of course, this is only enough to keep you $1000~\text{ft}$ above sea level. If you want to float above the tallest building in the mile-high city (or get from one side of the US to the other) you need to have $\Delta z = 4000~\text{ft}$ high balloons.
Psuedoscience (Aside)
It looks like we need to ignore hard-science if we want to make this work. Personally I would have your city levitated with a variant of a reactionless drive. The common spaceborne sci-fi variant pushes on a gravitational well, so that momentum is conserved but no reaction mass is expended. If this is possible, it may also be possible to "latch on" directly to the gravity well of a planet. It would essentially be a floating solid foundation (although it would experience tidal motion due to the influence of the Sun and Moon). The energy requirements would be zero until the city moves, and when it does the required power can be made as small as desired by reducing speed (although the total amount of energy required to lift the city a given height is fixed by its weight).
Generic Problems
Whatever method you use, there are two more problems that I can foresee. First, your city will be a giant moving eclipse. Nobody wants an airship the size of Guam floating over their heads, even if it's just for a day: not cities, where there are lots of people to get angry; and certainly not in rural areas, where crops could be harmed by the lack of sunlight. Environmentalists will protest the disruption to the local ecosystem wherever you go.
Second, wind speeds increase rapidly with altitude, and temperature and pressure decrease; not to mention that low clouds would pass through the city like dense fog. Inhabitants of a floating city would experience worse weather than ground-dwellers at pretty much all times.
Thirdly, the city would likely be subject to electrostatic charging by the same mechanism that causes clouds to become charged. At the very best, the city itself would act as a lightning conduit during storms. At the worst, the city itself might generate a few small lightning strikes when first passing over a tall building. (Yet another reason to refuse passage to this power-hungry/regular-hungry darkness-bringer of a city.)
Pretty much all these problems can be countered by floating close to sea level above somewhere with no people or plants. But in that case, they'd probably just drop it down the last 100 feet and float it on the ocean—much easier.