Am I missing something?
charging up a R/C/LED circuit at Vcc is very much like charging up a R/C circuit with Vcc-Vfwd where Vfwd is the forward voltage of the LED.
So 63% of Vcc in this case (about 3 V) should really be compared to time constant of 3 V under a Vcc of 5 V - 2.2 V = 2.8 V < 3 V. Which is very very long, as you observed.
edit: here is a quick simulation that may help explain the difference between a rcled and rc circuit.
The circuit on the right is a rcled being charged up at 9v. the circuit on the right is its equivalent rc circuit being charged at Vcc - Vfwd. The curves are roughly the same - but not exactly due to the much higher equivalent resistance of the led as charge current slows down.
hope it helps visualize it for the OP.