How much are you willing to change cities? Are we talking about retrofitting existing cities to better handle hurricanes, or building brand-new ones specifically engineered to be hurricane-resistant?
There are two key weapons a hurricane uses to cause damage. Let's address each in turn:
This is the defining element of a hurricane, and the primary cause of damage. The winds are generally strong enough to break trees and send unsecured objects flying at high speeds. How can we make our cities more wind-resistant?
1. Minimise debris-forming structures.
Road signs, house siding, tree limbs...all these and more can become deadly projectiles in hurricane-force winds. Our hurricane-proof city should minimise all such loose material, replace signs beside the road with signs painted onto the road. Keep light vehicles (cars and motorbikes) inside sealed garages.
Dome-shaped structures are ideal for surviving strong winds - traditional flat-sided buildings present a broad flat sail to the wind, which can and will build up enormous pressure on one side of the structure, often leading to catastrophic collapse. Domed structures, with their sloping walls, have no sail area at all, so the wind simply blows over them. They also present a stronger face to any wind-borne debris. Existing structures could be housed within domes to prevent future damage.
3. Storm shutters.
Of course, you can't eliminate flying debris entirely, so you'd probably want to make sure every structure had steel shutters that could be closed in the event of a storm to prevent windows from being smashed.
4. Elevate critical transportation arteries.
We saw in hurricanes like Katrina and Sandy, cleanup and rescue after the storm was hampered by damage or flooding of critical transport routes. Keeping a few arteries, like highways or rail tracks, a few metres above the surrounding terrain would make them less likely to collect debris, and easier to clear.
1. Build underground.
A city built beneath ground level would be largely immune to high winds, which would simply skate over the surface without touching the majority of the structure. The surface footprint of such a subterranean structure could be in the form of a dome, as well, providing all the previously-mentioned benefits. Transportation networks could also be kept underground, and impervious to wind.
2. Wind baffles
This is a less practical option, but it could work on a large enough scale. Essentially you would have the city surrounded and filled with large concrete (or magitech) baffles which could rotate to face the oncoming wind, effectively lifting the wind above the city and reducing the wind speed on the streets. This would probably be very expensive, though.
In some cases, the storm surge associated with a hurricane can be more devastating than the winds themselves. Storm surge is a sudden rise in sea level caused by the winds blowing additional water ahead of them, and if low-lying parts of a city can be penetrated, they can be deadly. Once water begins flooding low-lying areas, it will likely keep going - and it won't flow out again of its own accord. It would need to be pumped out.
The brute-force approach. Levees are earthen embankments build to keep high waters away from an urban area. They're frequently used on rivers and canals, but they're also used in places to keep the sea back (see dykes in the Netherlands, etc). They're cheap, but once a levee is breached things are quickly going to get very bad.
2. Build high and strong.
Flood waters can be deadly. They carry debris and disease, and can quickly overwhelm and drown unprepared citizens. Thus you'll want to be sure that everyone has some high ground they can easily reach. The easiest high ground, of course, would be the upper storey of their own homes, so all houses should have at least two storeys. They should also have a way to get out of the upper story, in case flood waters begin to rise even above that point - in Hurricane Katrina, many people were drowned in their own attics because they could not get out. This is another case where building elevated infrastructure would help.
3. Flood gates.
These are the more advanced relatives of the levees mentioned earlier. Flood gates are literally heavy gates that can be closed across choke points like harbour entrances to keep high waters from passing through into the populated area behind. They're expensive, and can't protect areas along a very broad front, but they are practical in some situations.
It sounds silly, but if you can't prevent flooding in your city (say, because it's built below sea level...), you can at least seek to minimise damage by ensuring that important utilities and documents are protected from water damage. It won't help in the moment, but it will make recovery easier.
One of the reasons that Hurricane Katrina was so devastating in New Orleans was that the water stayed in the city for so long, and this was because the city's pump stations mostly failed. These pumps drew water from drainage canals and dumped it back into Lake Pontchartrain. Unfortunately, the pumps were not themselves waterproof, so when their motors got wet they became useless. Waterproofed pumps would be essential for clearing flooding quickly from the city.
1. Don't build your cities below sea level.
It's just never going to work out well.
If you built underground, this is especially important. You'll do all you can, of course, to keep your structures sealed against the water. That would include several sets of heavy steel doors to close against the outside, etc. But in the event that a structure is breached and begins to flood, you need to be able to seal tunnels that connect your underground structures to prevent the flood from spreading. Heavy steel sliding doors should be able to do the job easily enough. Ideally, they'd also have airlocks built into them so that the population of a flooding structure can be evacuated to another structure without opening the main doors.
3. Don't build your cities below sea level.
I don't think I can stress this enough.