Sometimes when planning we get too busy studying the trees and miss the forest, too.
Make sure to consider all costs involved for a trip. For example, if you're flying to a big city, then yes, maybe the fees are high. But maybe you won't need to rent a car, if other transportation options exist like a hotel shuttle. And if you don't have to rent a car, then you don't need to pay for car parking at the downtown hotel.
And then there's the convenience factor. "Busy" FBOs (i.e. often the expensive ones) are often (but not always) pretty well set up to get you in and out quickly and on to where you're going. You may spend longer trying to arrange fuel and transportation at the small, uncontrolled but cheaper strip. Or, the small strip might be more convenient and have shorter taxi times with no ATC delays. You just need to check ahead of time.
And maybe if it's just you traveling, you're okay with "I just need a self-serve fuel pump and a porta-potty". But if you have non-pilot passengers, they might like a few more amenities (like free cookies and indoor plumbing). Makes them feel fancy. And don't forget, if they like flying with you, they're more likely to want to go more often - what's that worth?