There are a few things working against you here. First, it is winter over most of the U.S. and as such cold weather, denser air, winter forumlation of gas and the the conditions of your commute all might be limiting your FE. There are very few of these items that you can control. So, I seriously recommend that you make sure that your tire pressure matches the spec that is on the vehical cert sticker on the driver's side "B" pillar.

Break-in is a reality with these vehicles. I figure that by the time you crack over 5k you will see some better numbers. Second, I'm not sure which trim package you have on your Highlander, and I'm not real familar with what mileage tracking there is on the Highlander, but if you have an onboard FE average calculator, compare that number to anything you calculate. You will be off by a few MPG almost all the time. However, an onboard FE calculator is much more accurate than your hand calculations because the vehicle is calculating FE based upon actual metered fuel. You calculate FE by comparing how many gallons you used between mileage points. The problem with that calculation is that each fillup is not necessarily going to fill the fuel tank to the exact same level each time you fill up. So, there is inherant variability in that calculation.

It has been said:
Hybrid drivers come in 3 flavors, greenie, techie and cheapie. Pick any 2.
2005 Prius, Melinium Silver over gray, package 5 (AI)