I commute either on the road(13 mile 1 way and hilly) or canal( roughly 15 mile and much more plesant if it hasnt been raining!) the canal route is a mix of broken track/cobbles and compacted mud.
I've got a Sirius bought with 32 armadillos on(no punctures yet 3 months), for speed on the road I put 23 gatorskins on(1 puncture in 5 months) for a while....I tend to use the bike more and more with the kids now and have put the 32s back on as we use canal towpaths and the 23s were too harsh and rubbish over cobbles.
The speed on the road equals about 5mins on my road commute but wuth a little more effort.....never mind I get fitter quicker and I'm only racing myself.
You dont mention what width the Trek comes with?
Give the armadillos or something with a little tred a go, if your wheels suffer over time have them retrued till they've had it then splash out on a posh new set....speaking as a tightwad.