Garbodor is 'unpopular' because it epitomises what is perceived by a lot of people (read, not necessarily me) to be one of the weakest generations in terms of Pokemon designs and ideas. Gen 5 gets a bad rap for using a lot of design concepts people disagree with, and the fact that generation introduced more Pokemon than any other perhaps has people under the impression they went for quantity over quality.
People often take issue with the designers taking inanimate objects and giving them anthropomorphic (i.e. human) features and calling it a day. So basically, people thought it was lazy and uninspired that they just take an ice cream cone and a bag of trash, give them faces and call them Vanilluxe and Garbodor.
From there on in, perhaps it's just become 'cool' to hate on Gen 5. This bandwagon, hive-mind mentality hasn't been kind to Garbodor nor Gen 5's designs, and it's ironic considering Muk is a very similar concept that doesn't get nearly as much hate. I wouldn't pay it too much mind, a lot of it is just people looking for something to latch onto and poke a bit of fun at.