Enable and disable power of USB hub in the Beagleboard XM

Ive detected that usb hub chip (is the chip near USB connectors) is
hot without any device connected.

Ive done this

cat /sys/bus/usb/devices/usb1/power/runtime_status

and the result is active, anyone have idea how check if the
autosuspend, and wakeup values are working properly
and how to control?

Hot is a relative term. Yes, that part will run a little warm. The longer you hold your finger on it the hotter it will get. You might try measuring the temperature. Typically it runs around 45 to 48 degrees C.