I am testing my ESP-WROOM32 based board, using a CP2102 USB UART with RTS and DTR control lines connected to EN and BOOT respectively.
On windows I can use mos to flash the module and the new firmware starts up and I can see the log messages etc.
On my kubuntu 17.04 VM it flashes OK but does not start up. The problem seems to be that the linux version of the tool leaves the DTR and RTS lines pulled low. This holds the module in reset. On windows the lines are released and go high.
The Espressif esptool works OK with the same board and the same USB UART on linux (make flash, make monitor etc).
I believe most development boards have an extra circuit to convert the "both lines low" state to "both lines high" so that it all works OK on these. See e.g.
But my board does not have the circuit, it was not needed before.