Kombucha can go flat because of a variety of reasons. Here is a troubleshooting guide.
Improper packaging: You need a proper container that can retain CO2 pressure. Crown caps are the best for it. However, screw cap type milk bottles don't hold pressure that well. A swing type bottle is also great. Priming Sugar: If you ferment the kombucha completely, then there is not much sugar left for it to ferment and carbonate. Use a hydrometer and add about 8gm of residual sugar per liter at the time of bottling. Improper bottle conditioning: Natural CO2 takes a couple of days to form. Keeping the kombucha in the refrigerator immediately after bottling does not give it adequate time to carbonate. Lack of yeast. If you filter your kombucha, then you might strip it of yeast and healthy microbes. This would not allow the fermentation to happen in the bottle.