You should have called and ordered. Some online checkout systems have either a minimum or a "guess-imated" weight per item. So the accumulation of 3 very small items gave an inaccurate price.
I have always found them to be fair and honest. In fact the following page on their site is devoted to the whole shipping question. http://www.cheaperthandirt.com/SquareDeals.aspx
I have dealt MANY times with them, as have many of my friends. I don't exclusively use them, as better prices can always be found if you shop around (sometimes at CheaperThanDirt, and sometimes at other vendors). The whole shipping concern, however, seems to be an unfortunate experience and not the norm.