Let's say you're writing a short story, like I recently was. Or you're writing your novel as usual. Inherent in every story are questions, like:
"Why is this character doing this?"
"Who is that guy?'
"What is that mysterious object?"
These are things you want to answer, but not always immediately. People want to know the answers to things, and so they will keep reading to find the answers, or at least see if the answers they thought of are correct. You want to put questions like these in the reader's mind. Some hidden motive or plot related element -- hell, even a red herring will do, though too many and your readers feel tricked.
Timing these questions can be tricky. You don't want to pose the question "who is this mysterious stranger, how did he save this guy" and then never answer it, unless that's the whole shtick of that character. There needs to be some sort of closure. The reader needs to be tugged along until just to the point of exasperation and then given that tasty morsel that rewards them for hanging on for so long, and then you hit them with a bigger question. I'm not going to dig too deeply into timing right now -- I'll save that for another blog post.
What I will dig deeper into is which questions do you answer? Which questions raised are the important ones to answer?
That, in itself, is a difficult question to answer. Something like "how does this mythical weapon return to its home after its owner dies" may seem like an important detail to you, but to someone else that's just something to handwave away. It's not plot-central, all that matters is that it does.
Writers can be a nit-picky folk, especially with their own works. We know our worlds inside and out, so when something doesn't quite make sense, we get the urge to explain it, to figure out how or why something occurs. Which is important to a broader sense of world-building, but it may not be necessarily important to the reader. Magic systems in fantasy are a great example of this. Some magic systems are very deliberate, with lots of rules and limitations, which for some readers gives a great sense of understanding, and helps to immerse them in the world.
Others might disagree, and prefer a less Brandon Sanderson style of scientific magic and more a Robert Jordan big handwavey magic where things just happen.
I realize I've strayed from the point of plot-related questions, but it's all parts of the same. When you're writing, you're crafting questions and answers, all to lead the reader to some sort of epiphany. But as many editors have said, the thing you think your book is about is probably the last thing anybody else will believe it to be. South Park makes fun of this with the episode the "Tales of Scrotie McBoogerballs," where people just read whatever they want out of a book of purely disgusting filth.
That isn't to say that you can't affect what people are going to get out of your book, but what I do mean to say is that you can't always predict what things are going to stand out to your readers. You aren't them, and they aren't you.
So my advice, overall, is not to worry about every question you raise. Some people aren't going to care what that mysterious guy in the shadow's motivation is. For them, it's enough that he's a spooky man in the shadows. But those same people might get incensed that you haven't properly explained how your gravity-defying zeppelins work. You can't decide what people are going to ultimately decide is important in your books. You can weight certain devices and plot elements but in the end your readers may just skip right over them and decide that the random homeless kid stealing an apple at the market is a much more interesting plot point and what ever happened to him?
Answer the questions that feel important to you. Then let other people read your work and see what they found was important. Ask them what they thought the plot hooks were. You may be surprised what questions you were really asking. Then smooth out the details. You may find that the subtle hints you were dropping over and over like bread crumbs, making a little plot-road for your readers to follow were totally ignored, while a bunch of random events you put in to sort of even out the story actually were more evocative for your readers. You can only learn from experience.
Sorry if this one was a little rambly, but I know that many of us obsess over what messages we're sending to our readers, and what questions we want them to be asking when they're reading. It's important to remember that none of us can fully predict that. We can try for certain things, but we're never guaranteed. It's all up to the individual reader to decide what our books mean to them, and why.