He gets to the line a lot because people intentionally foul him because he can't hit free throws. Teams score on slightly more than half of their possessions and you have to throw in some three pointers. If Jordon only hits 50% and I'm giving him the benefit of the doubt there, you are destined to lose every time teams take to fouling him intentionally.
If he was the defensive presence of early Shaq, then maybe you could live with it, but he isn't.
But, even if he only makes 1/3 of his FTs, the sheer amount of FTs he takes would up his points per shot in his optimal zone to one of the highest in the league for centers. He gets about 1.5 zPPS. Not exact, but it's rounded. Howard gets about 1.7. Only a 0.2 point difference per shot in their respective optimal zones (which happen to both be in the paint), and that is with Howard getting nearly as many zFTA as zFGA. If Jordan could miraculously hit 50% of his FTs, as you suggested, it would move it up to about 1.55 zPPS, putting him that much closer to Howard and other elite centers.
Also, yes, as people have mentioned, you would be wise to stack the zPPS against how many points per possession they give up. There's a site that lists them for all players, but I can't find it.