When it knocks out saved passwords seeing a need to re-enter user names and passwords constantly you can understand why many would prefer to simply uncheck those items. As for cleaning up IE histories there are some other utilities that will do that easy enough.
When first trying it out and wondering why cookies as well as other are being wiped one expression would be: "what's this? I thought thiis was a drive cleaner not an IE cleaner!"
Here I may end up wiping a partition anyways and use it every once in some lengthy period. Every so often when everything like IE favorites and llinks get the periodic backup as well as simply dunping a few saved I'll check off everything when going to run it then.
For a thorough cleanup programs like Evidence Nuker and other security apps actually perform far better for removing traces of where you've been in that sense. Those are also useful when going to sell or trade used systems too.