I'm with @Charlaquin on this one, myself. To me, all Hunter's Mark is doing is making it easier for you to make better hits on the creature (the same way critical hits and Sneak Attacks are better hits.) That's pretty much what the spell description tells you what you are doing-- you are Marking the target and thus merely enhancing your divination sight to make it easier for you to make a more powerful hit. The spell itself isn't causing any direct damage, it's allowing you to make better attacks. So that by itself does not require me to make any "great leaps" in logic or intuition to suggest the extra damage is not any different than the base damage (just like crits and SAs are not different). You merely can now see the target better and thus your standard attack has a better chance of doing more damage.
Now that being said... I also have no problem accepting the other side of the argument that the intention is that the Mark damage is magical since it comes from a spell. That also is a completely understandable reading of a possible generic rule of D&D-- anything involving a spell makes everything that's a part of it automatically magical, including damage that results from an effect that increases your ability to perform. Even if the spell itself is not the direct cause of said damage.
But without this assumed generic rule of D&D that says anything related to a spell effectively places the "magic" tag on every effect or result that comes out of it... the former interpretation to me makes just about as much logical sense as the latter does. But of course I don't care either way, because when the time comes to rule it in my games... I'm never going to waste time arguing with my players about it. Yeah, take the 1d6 magical Hunter's Mark damage. That's fine.
Now that being said... I also have no problem accepting the other side of the argument that the intention is that the Mark damage is magical since it comes from a spell. That also is a completely understandable reading of a possible generic rule of D&D-- anything involving a spell makes everything that's a part of it automatically magical, including damage that results from an effect that increases your ability to perform. Even if the spell itself is not the direct cause of said damage.
But without this assumed generic rule of D&D that says anything related to a spell effectively places the "magic" tag on every effect or result that comes out of it... the former interpretation to me makes just about as much logical sense as the latter does. But of course I don't care either way, because when the time comes to rule it in my games... I'm never going to waste time arguing with my players about it. Yeah, take the 1d6 magical Hunter's Mark damage. That's fine.