You didn't provide a lot of details, but I'm going to assume you are using a WiFi adapter with the Realtek 8192cu chip, since that seems to be commonly used. Mine is the same and I have been experiencing what I think is the same issue: when leaving the RPi idle for an extended period of time, the WiFi seems to be disabled and you can no longer connect via SSH, etc.
I have been searching for a solution to this for months and only just now found one here: https://github.com/xbianonpi/xbian/issues/217. The solution is for xbian, but it worked for me on Raspbian.
The problem seems to be that the adapter has power management features enabled by default. This can be checked by running the command:
A value of 0 means disabled, 1 means min. power management, 2 means max. power management. To disable this, you need to create a new file:
sudo nano /etc/modprobe.d/8192cu.conf
and add the following:
# Disable power management
options 8192cu rtw_power_mgnt=0
Once you save the file and reboot your RPi, the WiFi should stay on indefinitely.