In new construction they can make a lot of sense. For replacement the cost can get up there. They use a lot of BTU's so in many homes the gas line needs to be increased back to the meter. Another con my HVAC guy talks about is using them where there is hard water. Mineral build up on the heating fins can create a maintenance challenge.
On the positive side, over time they are easier on the gas bill and can handle large demands if sized properly. Just be sure you don't try to do too many things at once. They can be taxed out if every tap is being used at once.