"Gomen" is used only for apologies.
If someone tells you bad news, to express sympathy you can say
- sorewa taihen deshita ne (it must be tough on you)
- okinodoku ni... (I feel sorry for you)
- zannen desune (you must be disappointed)
just for example.
Of course, souka... (or more politely, sou deshitaka...) is also good when you don't know what to say.