People treat WordPress like a Swiss Army Knife because they can. Why build an online directory or CRM or auction site from scratch when you can just use WordPress? It can be a bit sloppy, code-wise, but it works and you can get the job done a lot faster than it would take to do it from scratch.
Consider an online business directory. You could just build one from scratch or use some script designed for that purpose but WP simply offers more flexibility. If you decide you want a Google Map displayed in each listing, just download the relevant plugin. If you want to add oEmbed functionality (for, let's say, embedded videos), it's already built-in. If you want to do advance taxonomy queries use the Taxonomy Drill-Down plugin, etc.
Yes, it's all held together with chewing gum, but it works.