Why are some seemingly simple sets, so expensive?
Without examples, it's difficult provide a precise answer, but I'll give it a shot.

Since you mentioned Amazon, I assume that's where you are getting your pricing information from. As you noted, prices from many retailers will fluctuate based on supply and demand, and that can often explain why a set is expensive.

Amazon in particular lists many sets which are no longer in production. As an extreme example, the UCS Millenium Falcon is currently listed at over $3000 USD even though its MSRP is just $499.99. Popular items tend to be more expensive on sites like Amazon after the item is no longer being produced by TLG due to shrinking supply.

You can search sites like brickset.com and others to find information about the year a set was released and its MSRP. In general, if a set was released more than 3 years ago, it is no longer in production and you will probably pay a premium to get it new and in its original box. You can also start by shopping at LEGO.com where all of the sets will be currently in production.