In my installation the Account Settings window has a 'Junk Settings' option. Mine is UK English, I guess yours may be called something different. Anyway within that option there are various tick boxes: a) to enable adaptive junk controls for the account, which means that Thunderbird will let you teach it what is junk mail and what isn't; b) to not mark mail as junk automatically if the sender's address is in a selected address book; c) to trust an external database (SpamAssassin in my case) to help determine what is junk from the subject line of the message. You need to set up those controls first. Then you need to teach Thunderbird. Each time it marks a message as junk it puts a 'junk toolbar' at the top which says 'Thunderbird thinks this message is junk'. There's also a button to mark it as 'not junk' -- i.e. to tell Thunderbird that it has made a mistake in this case. If you keep correcting it the accuracy of its detection should improve. It may never be 100% perfect, though: if a trusted sender writes to you about diet pills or investment opportunities, Thunderbird may still be inclined to treat the message as junk simply because of the subject line.

Thanks. This was very helpful and seems to have solved the problem!