Although kingofnarnia's method totally works, I find I have an easier way of changing things this way--

Instead of going into each class's config individually and pasting cl_autoreload 0 or 1, make a new config file called "default.cfg". In this file, you put in everything you want as a default set up (i.e. fov_desired 90, cl_autoreload 1).

Then, for each class config (i.e. scout.cfg), include the line "exec default" and when you choose that class, the settings listed in default will apply.

THEN, for the classes you want to be different from the default setting, you individually type in something like "cl_autoreload 0" to the class config. Typing in "cl_autoreload 0" after the "exec default" line will override whatever setting you had in default.cfg.

I use this method to change around my autoreload, but also for different sensitivities between classes. I play scout/sniper with a much lower sensitivity than when I play soldier, for example.