The biggest problem of the french railway system is that it is centred arround Paris. It means doing Toulouse Marseille by train might take you up north in Paris. Car is a good thing, despite that french police is very strict. And it is not cheaper than renting a car I belive as train tickets costs about 100€
If you plan to visit entire France, the car is the best way. You can drive and stop whenever and wherever you want. Week ends of July and August are a nightmare on french roads though. And gas is very very expensive
Train offers a wide range of possibilities, especially when you take the TGV ( high speed train ) for long trips. Paris is 3 hours from Marseille. You can walk and enjoy your trip. Stations are well organized, with regular buses and taxis in big cities. However when there is a strike ( 22 may 2008 for example) they are a lot of cancelling and delays.
Bus is very very tiring as it does not stop often and you can't walk in it.
You'd better draw your trip and consult SNCF website as seles told you to manage and verify the connectivity between your way of transport.
If you want to travel in France, the best way is to rent a campervan. "Van-It" is the first company renting campervans in France. Theyre located in Paris and rent really cheap Volkswagen Californias. Have a look at their website : www.van-it.com