Sadly the number of cyclists who either nod , smile or wave any thanks is, in my experience virtually zero [as opposed to drivers, m/cyclists or even horse riders]
As above he may just have been cream crackered but if you're expecting any appreciation - forget it.
I think thanks is appropriate when you're being genuinely considerate (allowing someone out of a side road when you have priority, for example).
For simply not putting yourself/someone else in danger, I think that it's questionable. Thanking people for exercising what *should* be the minimum standard of driving/cycling/walking always seems a bit weird to me, although I have done it myself at times.
"Thanks for not killing me!"
"Thanks for not piling your car into oncoming traffic due to your baffling impatience!"
One other point is that even considerate motorists are often quite far removed from recent experience on a bike, and their actions are taken from a "car" point of view as a result (one can be quite sanguine about distance and speed when surrounded by a lot of protective metal). Mrs M and I had a discussion on this recently when she was driving - she followed (imo) too close to a couple of riders we encountered before making a (safe) overtake. In the cyclists' shoes, I'd have viewed following so closely as a "hurry up" from the driver, and not been happy (as well as worrying that it meant a loony overtake was coming). If the OP had left less than, say, a car length or two, that's a possible reason for the scowl as well.
Incidentally, around here, horse riders tend to be pretty haughty types, and you're as likely to see an Audi driver using indicators[1] are you are to get an acknowledgement from our equestrian road users.
[1] Using them as hazard lights while parked illegally excepted.