Trying to understand the purpose of the capacitors and resistors in this bus powered configuration for the FTDI chip, I think the capacitors are for filtering high frequency noise, not sure what the resistors for though, maybe line termination ?
The series resistors are for line termination. From http://www.semtech.com/images/datasheet/usb%20line%20termination%20_ag.pdf
The Universal Serial Bus (USB) line termintation is specified in the USB 1.1 specification to insure proper terminations so that signal integrity is maintained. The termination requirement varies depending on what driver chipset is used, whether the port is upstream or downstream, and if the transceiver operates in full or low speed.
When the USB 1.1 specification was written, a series resistor between the range of 28Ω to 44Ω was required. Most USB drivers will require a termination resistor of 16 - 33Ω.
This is in addition to the pullup/pulldowns used for identification.
The caps are used to ensure the line meets the required rise/fall times as well.
The resistors end up both helping prevent ringing (by making up a RC filter) and electrically protect the input, as well as impedance match the end of the long wire. They may also help guard against load dump when the connection is hot disconnected.
The smallest cap across vcc/gnd seems useless given that there are already a ceramic and an electrolytic there. Those are there to manage load dump during hot disconnect as well.
The inclusion of the two capacitors to ground before the termination resistors is a bit unusual. Typically the goal is to minimize stray capacitance to ground before the termination resistors to minimize the impact on signal integrity. According to FTDI app note AN232B-06 (found here http://www.ftdichip.com/Support/Documents/AppNotes/AN232B-06_11.pdf ) page 10:
Some USB 2.0 hubs appear to be extremely sensitive to noise. A glitch on the USB lines can in some cases cause a device to hang. This problem can be fixed by adding two 47pF capacitors to ground on the USB DP and USB DM lines. These should be located between the 27[Ω] series resistors and the hub