I believe the reason they do the minimum charge is because of the fact that banks tend to siphon off some money for each digital transaction- most likely it works that way because steam is such a large platform. Anyway, as a result, anything lower than $5 basically isn't worth their time.

I recall hearing a way to add funds that were lower, though- I nosed around. Basically I think it runs down to being able to charge close to an exact amount by attempting to buy something with insufficient funds (it prompts you to add exact funds as you check out) or you can manually charge the exact amount though use of java, though I'm not sure how that works, or if it's allowed. I haven't tried either method, myself.

Those tips are discussed a bit here:
http://forums.steampowered.com/forums/showthread.php?t=1485923

The steam forums can probably tell ya about steam stuff better than the SK forums! I hope this can help. I'm really unsure about the java one, though (you might want to look around and see if anyone's gotten banned for it before), so use that at your own discretion.