I just bought a house and in the basement the single wall furnace flue is touching the dark iron natural gas pipe, just before it enters the brick chimney , the water heater also has single wall flue that runs through wood structure. The previous owner put coffee cans around the flue, he cut off the top and bodoms of the can and slid them on the flue, I think he did it for Heat Dissapation. Is this safe having them touch?

It would be better if you kept something non -flamable between them you never know what could happen with two pipes touching... but in my home w have pipes that cross coming from the furnace but never the gas line

Sounds like you have at least a couple of major safety issues that need to be addressed as soon as possible before you have a major catastrophe. Flue lines in direct contact with flammables (wood or gas) can never, ever be a good idea. If this were my house, I would disable both the furnace and water heater until a competent (licensed) home inspector (familiar with local codes) gave the house a complete going over. It has been my experience that houses with 'make-do' owner installations and repairs likely have other - often hidden and potentially dangerous - problems in the wiring, plumbing, etc. Why risk the lives of you and your family? Have it inspected today! Anyone on this forum who offers different advice than this is dead wrong.