Like many things in the energy efficiency world, the real answer is it depends.
For example what type of heating system do you have?
- A radiant floor system will take time to bring the floor and areas back up to temp - is this wait something that you can live with?
- If you happen to have a heat pump system you could have another issue with the system turning on the emergency heat strip which will kill any savings you might have gained.
- Another question deals with not only the age of your house, the type, but where do your water lines run?
- While shutting down the heat should not matter in most cases, there are times that the only reason they don't freeze is because of the heat from the house
As a rule of thumb though, in many cases you probably will save some money.
I am assuming your timer is a programmable thermostat, if not may I suggest you get one or maybe even try a NEST system that will learn your patterns and possibly save you even more money.
For more information:
Read "How much energy savings do you get by turning a thermostat down 5 degrees rather than turning it off completely twice a day on a timer?" a Q&A answered by David Willson.