Your crystal loading cap values are way too high (100nF!). They are usually in the tens of pF range. Check here for how to calculate a value for your crystal:
https://blog.adafruit.com/2012/01/24/choosing-the-right-crystal-and-caps-for-your-design/You also need more decoupling caps, usually a small one (~100nF) for each power pin, and a bulk (~1uF-10uF) cap for each chip. The 3V3OUT on the FT232R also needs to be decoupled. Check the reference design for each chip for the recommended decoupling configuration.
The reset pin on the FT232R is internally pulled up. You can either leave it unconnected or use a resistor to pull up to vcc. Shorting it to vcc could interfere with the chip's internal reset generation.
The reset pin on the atmega could tolerate up to 13V, do you need D1? You need a series resistor anyway if you want to use D1 for clamping, like this:
@cowasaki you don't need the 47pF decoupling caps on the usb data lines