I'm sorry to hear you had a bad experience. I have nevered had a problem ordering fabric online and I've been doing it for several years. However, and this is a big however, I never use a company that doesn't already have a good reputation or doesn't come with a good recommendation by quilters I trust. You'll never go wrong with Keepsake Quilting or Connecting Threads without them making it right.
I imagine what happened is that you were sent the poorest of the dye lots, which is the first one & usually the worst when it comes to the colors not matching. I would suggest not ordering fabric from there anymore. You've mentioned your LQS was able to help you salvage your project so I would guess you don't want to contact the company and return the fabric. I hope you do not let this one bad experience turn you off. Stick with the more reputable companies and enjoy the benefits that online shopping can provide.