Yeap, this is indeed the big issue. One thing that helps is to tune the UI for your specific domain so that it has just enough power to be usable in that domain, but no more. We had to build a query tool for retailers in my last gig, and tuning the UI just for retail helped a lot.
For example, make it easy to specify a BETWEEN operation in your UI if that tends to be used often, provide commonly-used domain queries as templates so your customers can learn by looking at and modifying these templates, etc.
For inspiration, you may also want to look at other products that have query building as core feature. Two that stand out to me in terms of usability are mixpanel and chart.io: https://mixpanel.com/segmentation/ (see "Goodbye SQL" section) http://chartio.com/product/tour (see "Drag and Drop Chart Creation")