There are a couple of issues here.
First, let me give some information on myself, my car, and my commute. I have an '04 HCH, with MT. My commute is 112 miles RT, with about 70 of it on interstate highways and 25 percent on country roads in the rolling hills of western NJ. Quite similar to what you have, it seems.
With spring/fall weather, I have come to expect about 55-60 mpg on this route. My driving habits falls into the 62-65
mph range, the roads are getting too congested to do much more.
Now, here are the factors/issues.
The tires may not be the correct tires. I believe (members please correct me), that there were two OEM tires, Dunlops and Bridgestone LRR tires. The Bridgestone B321s can be ordered on-line for about $77 each. I have only used the Bridgestones, and I believe that they have one of the lowest LRR rating. More roll and less resistence. If you are really interested in the car, you could challenge the dealer to put the OEM tires back on (they can probably use the tires for another car).
Second, you may have fallen a victim on the tank MPG of the tank-to-tank spikes we all notice. Sometimes, you just can't predict exactly where the gas pump will stop pumping when it senses full. These type of errors can lead to sporatic jumps and dips in mpg, but they even out in the long run. On my HCH, the dashboard reading (OSD) always reads about 5 percent higher than my actual (your results may vary).
I will guess that the air filter is probably new (as a dealer should have done that type of routine maintenance), but if the dealer changed the oil, they might not have used the special Honda oil (0w20). Changing that to a synthetic oil may also help.
Given what you have told us, I think you have the potential to improve on the 44.5 mpg you got, especially on the run you have. You'll get used the the controls and gauges and "make" the car work better.
Welcome to GreenHybrid.com, I hope this information helps.