[susan53]

There's no rule for commas with co-ordinators when they join clauses. You could write eg in an email :
Sorry John. I was going to come to the meeting but I have the flu.
or
Sorry John. I was going to come to the meeting, but I have the flu.
Generally though, commas would be more usual if what came either or after was particularly long and complex, in order to give the reader a pause:
John and his family had wanted to visit the museums in Rome on their holiday, but they all caught the flu and spent the whole week in bed.
Notice the comma before but after the long statement but not before and after just a short one.

The only "pure " single words co-ordinators are and, but and or, though there are also correlative co-ordinators like either/or, not only /but also made up of two parts. The tests for the single word co-ordinators are that :

1. They can join not simply clauses but also other items of the same word class - eg two nouns - fish and chips; two adverbs slowly but surely; two verbs - sink or swim

2. They can never precede each other.

3. They can precede subordinating conjunctions : He was tired and although he wanted to see the film, he decided to go to bed.

4. They can only occur between the two items they join, and never in any other position.

So is technically an adverb not a co-ordinating conjunction. Notice that it doesn't meet condition (2) above. Eg : he was tired and so he decided to go to bed. is fine. [/i] But it is often used like one in more informal writing where a comma reflects the sort of pause a speaker might make : He was tired, so he decided to go to bed. But I'd avoid this in formal writing such as academic essays, job applications etc.