Of course you can compare Jordan and Kobe. Kobe's among the top 20 NBA players of all time, so it's not as if it's unfair to compare MJ to Kobe. Laker fanboys are annoying as ***** though, so I can see why there can be resentment there.
One of the reasons Jordan is so great (that rarely gets mentioned) is that if we look at the teams that have won NBA Championships, we see teams that have at least 1 very good to great 4 and/or 5, Jordan didn't have that until the 2nd 3peat and even then Rodman was almost non existent on the offensive end.
and the list goes on... The teams the Bulls defeated en route to winning Championships had a HOF 4 and/or 5; ATG 4's and 5's were getting ousted in those Championship runs. The list of 4's and 5's Kobe's teams have had to face in comparison really illustrate the point.