My understanding from watching all the various Star Trek series, especially TNG, is that there is a big difference between food that is grown, and food that is replicated. These are significantly different processes.
Variety is the Spice
Food that is grown is produced organically over time. In a real steak, all the molecules are slightly different, due to the organic, chaotic process by which it was created. Every one of these steaks is different, due to the different DNA of the cows involved, and the variance between each of the cells in an individual steak.
Food that is replicated is produced in an instant from a blueprint. Each steak produced will be essentially identical, and I presume that each molecule in the steak is essentially identical as well (obviously there would be multiple different types of molecule, but I mean that all the "internal red meat" molecules would be the same, and all the "external slightly singed gristle" molecules would be the same, etc).
This means that a real, organic steak would have a comparatively interesting and unique flavor profile, whereas each replicated steak would be just like the one you had last week. Even if a particular organic one isn't "better" per se, the monotony of replicated steaks would wear on a steak enthusiast.
Precision is Key
There's also the issue of replicator precision.
Wikipedia cites the Star Trek: the Next Generation Technical Manual as saying that
though the replicators use a form of transporter technology, it's at such a low resolution that creating living tissue is a physical impossibility.
This is the explanation for why you can't just replicate people. This implies that there are certain details of living, organic matter that the replicator can't accurately reproduce. Seems reasonable that this might affect the taste of any replicated organic matter.
The Wikipedia article on replicators goes on to say that
For example, to create a pork chop, the replicator would first form atoms of carbon, hydrogen, nitrogen, etc., then arrange them into amino acids, proteins, and cells, and assemble the particles into the form of a pork chop.
This process requires the destructive conversion of bulk matter into energy and its subsequent reformation into a pre-scanned matter pattern. In principle, this is similar to the transporter, but on a smaller scale. However, unlike transporters, which duplicate matter at the quantum level, replicators must be capable of a large number of different materials on demand. If patterns were to be stored at the quantum level, an impossible amount of data storage (or a set of original copies of the materials) would be required. To resolve this, patterns are stored in memory at the molecular level.
and finally
Though usually undetectable to human senses, computer scanning can be used to reveal these discrepancies, and they may explain the frequent complaint (by some gourmets and connoisseurs) that replicated food and beverages suffer from substandard taste.
Summary
So it's essentially the difference between a hand-crafted boutique product and a mass-produced one.
Each organic piece of food varies according to the whims of biological growth, unlike monotonous replicator products, and the organic food has higher complexity and detail compared to the imprecise replicator copies.
