The City of Ember is, you guessed it, about a city named—drumroll, please—Ember. But why call it that instead of Lina and Doon's Excellent Adventure or Lina in Emberland? One reason is that the mystery of Ember is bigger than both Lina and Doon, and it'll take them working together to figure it out. What happens to Ember is about more than Lina and Doon's fates, too: there are hundreds of people living there, and all of their lives are in danger because of Ember's failing infrastructure.
It's also worth remembering what the word "ember" means: it's a small glowing fragment from a fire, like a piece of wood or coal that's been lit and hasn't gone out yet. With this in mind, can you see why the Builders would name the city meant to preserve the last remainders of humanity "Ember"? Although it is a bit ironic, given how no one in the city uses fire on a daily basis, and in fact no one knows where fire comes from or how to get it to stay burning to provide light and warmth.
See, that's the thing about humanity as a whole in The City of Ember. They're great at starting stuff, but not so good at preserving or maintaining it. Like, it'd be great if we could come up with a sustainable way of life that doesn't destroy us or the earth. But in The City of Ember, people apparently mucked that up, so it's back to the drawing board to start over with a smaller-scale civilization. Hopefully Ember—representing the spark of life in its first stages—will be nurtured into a flame (a.k.a. a culture) that can provide warmth and life, without growing into a destructive, raging fire that consumes everything.
Another reason Ember is featured in the title is that it is a unique kind of city, and this fact is important to the plot of the book. If a normal city's infrastructure goes out, well, people are unhappy and try to leave and it kind of sucks but most people survive and move along to the next town down the road. But in Ember, if the power goes out, everyone is left in total darkness, unable to see anything or anyone. If the food runs out, there is literally nothing to eat.
The fate of Ember is central to the book's plot, then. But we also learn, throughout the book, that the city has a different purpose than the ones its residents assume. The city may, in fact, have saved humanity from extinction. But we'll have to read the second book in the series, The People of Sparks, to find out what happens to Lina and Doon and the others in the world above.