Every morning I make coffee with aeropress, fresh bean grounded with automatic burr grinder. When it is working day I would put it into a warm bottle and drink in office. I would arrive at office and drink the coffee around two hours. When it is holiday I would drink it immediately at home. Somehow I think the coffee taste not as good when I drink it in office. The coffee would have less acidity and a little more bitterness. I use a zojirushi warm bottle.
All coffee changes taste over time - it is full of relatively fragile organic compounds that will change over time.
Even in a vacuum flask (without exposure to light), the coffee will keep chemically reacting with itself. There is also oxygen in the bottle which will aid the breakdown of various of the compounds.
There really is no way to perfectly preserve the taste of fresh coffee unfortunately!
This is an issue not isolated to any particular brewing method. I cannot tell you specifically the mechanics behind why, but after you brew coffee, flavors will begin to be muted, heavy.. altogether unappetizing the older it gets. My understanding is coffee is both an emulsion and a solution. There could be some separation of the emulsified coffee oils over time which could result in the negative flavors, or simply degradation of organic compounds, oxidation of oils over time.
Long story short.. you're stuck with this, and you will be very rich if you figure out how to prevent this!