You absolutely can get 40MPG in a Civic. You can in a lot of small economy cars. The Corolla too.
We have a Prius too, and your assessment of the mileage is correct. The mileage is great, but if you are only concerned about absolute lowest operating cost, your money is better spent on a Civic or Corolla, Yaris, Fit, etc.
i get 28-29miles on highwAY on my is250 awd, which is 2,5 engine plus all wheel drive, so you probably can get around 40 mpg on civic with 2.0 engine,front wheel drive