It's quite likely that any or all of the teams will be chased by Death Eaters at the time of reaching their assigned safehouse, and you can't Disapparate directly from inside those protections. It's true that it would be needlessly risky to leave the safety of the protection spells again in order to Disapparate, for however short, with the possibility that it's swarming with Death Eaters out there. Much safer to stay within the protection limits and take uninterceptable Portkeys.

Mundungus' inclusion is explained by his having come up with the plan in the first place (courtesy of Snape), I suppose, though it's true they could still have replaced him.