Some of things that newbie cyclists often do that make it harder than it should be:
-- They mash their pedals rather than spin. You should aim for spinning your pedals at 90 rpm or higher. Mashers -- that is, cyclists who push big gears at a low cadence -- tend to tire out quicker and injure their knees. There are always exceptions, but in general spinning is much easier on your body and will improve your endurance more.
-- They ride bikes that aren't set up properly for them -- that is, saddles too low (rarely too high); handlebars too low (rarely too high); stems too long; saddle too far forward or back. Have an experienced person at a bike shop check out your fit. That could be the source of some of your problems.
-- They don't warm up enough. You should pedal easy for at least the first 5 minutes of riding. Hammering as soon as you get on your bike is a great way to get injured (and tire out), particularly if it's cold outside.
-- They don't wear the right gear. Cycling shorts, shoes, jerseys do make a difference. They are more comfortable and aerodynamic, and dry quickly.

Also, it might just take time to get into shape. You didn't say anything about your level of fitness. Many new cyclists are former runners or swimmers who already have the aerobic conditioning, so they can work up to faster and longer rides fairly quickly. However, if you seldom excercised before you started bike commuting, you probably are just out of shape.