Bah, I feel like everyone is missing a huge, huge point here.
One thing you have to keep in mind about the Federation is its generally an idyllic socialist like society. All that is made possible by technologies similar to replicators.
That being said, replicators don't just "beam" things out of thing air. Starships have a very complex system by which matter is recycled. Replicators resequence inert recycled matter from one substance into another. It's quite literally a form of what some might call alchemy.
The problem is there is a limit as to how far one form of matter can be resequenced from one form of matter into another form. I've always understood there is a physical tolerance point of how far something can be transformed.
That being said, I'd also suggest that may items that are replicated likely do not have the same quality of things that are hand made from the original products. A possible example that springs to mind might be something like clothing. Clothing that is replicated may literally start to fall apart after a week or a month making a genuine article more desirable. This would explain why many products for engineering can't be replicated --- their probably not able to replicate something with enough tolerance to withstand industrial wear and tear.