Ok, you have the MCU Reset tied to 3.3V. It should be connected to 3.3V via a 10K resistor. The ISP programmer needs to be able to pull it low to program the card. The FTDI chip would normally use one of its GPIO pins to create a level called DTR during a serial download, that level could connect thru a 100nF cap to Reset as well, which would kick off the bootloader & start the serial download process.
Test with an LED/resistor on pins 7, 14, 15,16.
Why do you have 27pF caps on the USB lines? That looks very odd. Series resistors, many parts need that, I can see that.
The datasheet does show caps, 47pF - but later diagrams dealing with battery charging do not.