It's easy to feel overwhelmed after a critique. We write a story feeling that we've communicated something vital, hoping that readers will connect with every word that we've written. When we discover that readers are confused, or that they’re less than enthusiastic about the work we've submitted, despair often follows. This is normal. I can't recall ever feeling particularly good about any critique I've ever received. I'll fight the critique in my head. I’ll question the judgment of the person who delivered it. Then, after a couple of days, I'll realize that the story I want to tell may still be powerful, but that my mastery of the craft has failed.
If readers aren't following, it's because you haven't led them. Every now and then you encounter a reader who won't be led, but most often, readers want to be led through a good story. If they aren't following, it's because you haven't yet discovered the way to lead them. Our primary responsibility is to guide readers through the complex world of our story. We do this by finding the right word/sentence/detail at the right time, the right path through the woods of story. Sometimes, we know exactly how to guide the reader; other times, it takes trial and error. Don't despair over the trial and error part; it's the nature of the process.
When reading the comments readers have penned about your story, it's important to remember that you don't need to act on every criticism or suggestion. Look for common threads in the comments. You've probably noticed (tearing your hair, screaming, banging your head against your desk) that some of the comments contradict each other. This is when paying attention to consensus helps. If a couple of readers object to something, it's a good idea to take a serious look at it.
Remember, however, that the changes you make don't have to be the ones the readers recommend. Often, when an editor tells me a particular scene isn't working, I'll decide that the problem isn't in the scene but in the setup to the scene, which happened a few pages earlier. Sometimes readers will make comments about your work that might apply to what they want to see developed in future chapters, not in the chapters you've just presented. For example, someone might complain that they don't know enough about one of your secondary characters. This doesn't mean you should stop the scene to drop in a detailed passage of back story about that character. Instead, you might insert the character in an earlier scene, or focus on developing that character a little more in a subsequent scene.
You will find that some readers know what you're trying to do and are helpful to your efforts to get there. Those are YOUR readers. Remember though, not all readers are your readers. Give serious consideration to those whose comments make sense to you, and put the rest aside.