You will eventually get used to it, but it never gets easier; you only get faster.
Do your muscles ache, or are they just weak-feeling?
You might try taking a few days off to rest your muscles. Make sure you're eating enough protein and drinking enough water. I stay away from the sports drinks. They're mostly sugar, which only provides short-term energy. You'll want to focus more on carbohydrates and protein for long term energy.
I've been riding regularly for about 15 months now. It took me a few months to build up to being able to ride every day. Even now, if I take a few days off (for bad weather, vacation, whatever) it takes a few days to get back into it.