You’re right, of course. Let me put down some numbers, for me and others—I just picked up this project again from where I left it last year!
A choice of R1 = 47Ω would limit the current to max 66mA (assuming D1 drops at least 0.2V, probably more during active charging) and dissipate max 0.20W. I’m not an engineer, but that looks a bit too close to 0.25W, so one would need a 0.5W resistor to be safe. Charging time (5×RC) of a 1.5F cap would be 6 minutes.
A choice of R1 = 100Ω will limit the current to 31mA, max power 0.1W, so a common 1/4W resistor would be fine. Charging time for 1.5F would be 12 minutes.
In the same manner, R1 = 220Ω will give 14mA, 0.04W and a charging time of half an hour.
As a bonus, all of these options are well within the 100mA max load of the 3V3 pin, so one could use the internal regulator to charge the cap (remember to sum all loads connected to the pin!)
I’ll go with 220Ω, because the charging time of half an hour does not bother me at all, and let you know how it performs in practice.