Free software licenses generally don't allow you to restrict who uses a piece of software distributed under such a license (see, e.g. Can I stop "evil people" from using my program? is the OSI FAQ). This clause allows you to separate your own identity from the software's, so that usage of the software can't be considered as a personal endorsement of some agenda you may not want to be associated with.
Let's take a hypothetical extreme example. Suppose you've authored a message board system that's licensed under such a license. You can't prevent the local Nazi party from using it, but this clause prohibits them from claiming that you support Nazism simply because they're allowed to use the message board system you've authored.