Resistance applies once per attack. Hunter's Quarry and Most Dangerous Prey should not be resisted separately.
From Player's Handbook 1, p104 (emphasis mine):
... Once per round, you deal extra damage to your quarry. The extra damage is based on your level. If you can make multiple attacks in a round, you decide which attack to apply the extra damage to after all the attacks are rolled. ...
Note that quarry damage is considered extra damage.
From Martial Power 1, p66 (emphasis mine):
Most Dangerous Prey
Against any humanoid target designated as your quarry, you gain a bonus to damage rolls equal to your Wisdom modifier.
Note that MDP damage is considered a bonus to damage rolls.
From the Rules Compendium, p222 (emphasis mine):
When most attacks deal damage, they do so through a damage roll: a roll of dice to determine damage. Whenever a power or other effect requires a damage roll, it specifies which dice to roll and how many of them. For instance, an attack might indicate that it deals 2d8+4 damage on a hit. When a creature hits with that attack, roll 2 eight-sided dice and add 4 to determine how much damage it deals.
A damage roll can be modified by a number of factors. ... The following bonuses are the most common for an adventurer's damage rolls:
- A specific ability modifier. ...
- An enhancement bonus.
- A feat bonus.
- An item bonus.
- A power bonus.
A bonus to a damage roll is part of the damage roll. It is not a separate source of damage.
From the Rules Compendium, p223 (emphasis mine):
Many powers and other effects grant the ability to deal extra damage. Extra damage is always in addition to other damage and is of the same type or types as that damage, unless otherwise noted. Because of this rule, an effect that deals no damage cannot deal extra damage.
Extra damage is in addition to other damage; it's bonus damage that you get as long as you dealt at least 1 damage.
When you an attack an enemy, all of the bonus damage and extra damage for the attack gets added to the attack's damage roll; the total damage for that damage roll is dealt to the target, and resisted, as a lump sum. Resistance is applied once to the attack, not once to each separate game element adding damage to the attack.
You should discuss how resistance is handled with your DM. If this approach is specifically intended to limit your damage, it's worth pointing out that rangers are strikers: their entire purpose is dealing damage, and they don't have much else to offer during combat, so you should be dealing significantly more damage than other non-striker player characters.
If your DM chooses to stick with their (incorrect) interpretation of resistance, then you should invest in a source of resist all yourself. Monsters don't get as many bonuses to damage as player characters do, but it will still be applied multiple times to some attacks by your DM's rules.