Yes, throw in some longer rides on weekends, preferably on a flatter route. I have a 3-mile commute as well, and it would have taken far longer to adjust without those weekend rides to build up the muscles.

I also recommend taking a day off from work commuting each week. Find another way to work and let your legs rest. It will make a huge difference in your energy level the day after. You don't describe in detail how big your ascent is, but if its significant consider taking two days off a week until your body adapts.

Wait awhile longer on the trailer, until you're comfortable with your daily commute, then start with weekend rides and see how it goes.