There are various reasons why a guitar may not play well when new.

Poor Setup from factory - Most guitar manufacturers do not put a lot of effort into the final setup process. This work takes time and precision. Large factories are concerned about the bottom line, and must turn out many guitars per day.
Poor fret work from factory - Many factories don't level the frets at all after pressing them into the neck. This leaves lots of room for error.
Effects of shipping and environment - Wood shrinks, expands, twists and flexes over time. Depending on the condition of the wood when the neck was made, the conditions it has been through getting to you, and the conditions where you are now playing the guitar - you may have some issues. Your guitar may have been built 18 months ago, shipped across the ocean on a boat, sat in a warehouse, and then hung on the wall at the store for a few months or shipped again bouncing around on a truck getting to your door. Don't be surprised if it encountered some issues. It likely needs some adjustment and definitely some new strings.
"Plek'd" at the factory - The Plek is a wonderful machine and does amazing work. Plek requires a talented operator to turn out good results, however. Not operating it properly can end up with poor fretwork. The setup is still performed by a person, and even though your frets might be perfect, the setup could be horrendous. (we've seen this a lot) There are some really great guitars being produced by several manufacturers with Plek, but there are also a few duds in the bunch. The effects of shipping and environmental changes still apply. The guitar may have been perfect, but again gone out of whack since the factory. It is made of wood, after all! If your Plek'd guitar isn't perfect, come see us.
"Inspected & setup in the USA" - This means someone took the guitar out of the box after it arrived from overseas and checked it out. If there were any major issues, these would be addressed or the guitar rejected at that point. This does not mean someone spent an hour or two dialing it in. The people who do this job will tell you it's usually only a few minutes per guitar. (they've got a lot of guitars to get through)
"Setup by the store" - Setup by.... the sales guy? Do they have a full time technician who is talented at setting guitars up? The person who sets up your guitar should be an expert at it. Otherwise, you may not be getting the full potential of your instrument. It's nice that they'll string it up and adjust the truss rod for you, but this free service is usually not quite the same as a full-blown job done by a luthier or setup technician.
My new guitar feels just fine - Great! You may not need anything at all. Feel free to bring it by and we'll give it a once-over. We'll address any issues we find. We'll also let you know if we can improve on the way it plays now. This inspection is free. If we don't believe we can make it play better, we will not pressure you to do anything. We don't want to charge money and not deliver a better playing instrument. We rely on the trust and repeat business of our clients.

So all this said - there's actually some companies that turn out very nice playing guitars. Unfortunately, these are the minority.

My guitar is new, why should it need a setup or fret dress?

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