Hmmm...well to some degree this gets into a matter of personal taste, intended use and bike fit. Just so you know I don't work for either one of these guys or sell their stuff. I just ride them, and work damned hard to pay for whatever I end up getting, or building. But I have a couple of Specialized bikes, and gave the Sirrus Pro a long, hard look. Long post to follow alert, but hey you asked.
The punchline with the Sirrus, even the Pro, was that I was really surprised and disappointed at the lack of quality in some of the components. To get comparable quality and function from Specialized, you have to move up to the Sirrus LTD version, with is about $800 more than the 7.7FX. Trek gives you some great gear at a much better price. Here's what I mean.
With the Trek, especially in your 2006 model, you get some really really nice gear. Both my 05 and your 06 come with the FX Alpha technology frame, which are really light but still very durable and stable on the road. They are well designed and surprisingly aero. That is the biggest surprise to me so far for this bike. You cannot get yourself in trouble on them unless you basically pull out in front of a dumptruck. They are that forgiving, even then you could probably juke/power your way out of it. This is a proven frame and design, with just the right amount of carbon too to give you a nice comfortable ride, to the point that they will spoil you. These bikes love to climb too, which is a blessing for a hybrid. Both the 05 and 06 versions come with good, strong, responsive brakes. Mine are especially smooth at slow speeds when maneuvering or like when slowing into a track stand. They are nimble too though when you need them to be and have saved my butt a handful of times already on commute, like at night when reaction time suffers in low light and you have to rely on improved response time from your components to bail you out.
I got the '05 7700FX with Deore XT (BEST) components, Bontager Race/Race X Lite (BETTER/BEST) and Bontrager Satellite Plus (BETTER) components. The wheels are Bontrager Select, which only top out their GOOD category; but they are plenty fast and they are frikkin bomb proof. They came with Bontrager Race Lite Hardcase tires which are an outstanding mix of durability, puncture resistance but still with excellent roll resistance (meaning they are definitely still plenty fast.) I commute on a combination of roads, bike route trails and even a bit of dirt trail. They hold up to anything and have yet to go out of true. On the road sections I can ride almost as fast as I can on my road bike so no complaints there either. No flats on them either.
In your '06 7.7FX, you get an even higher end mix of components. All in the BEST or BETTER category. Your Ultegra and 105 drivetrain is terrific and the upgrade of the wheels to the Race version is exactly the kind of bang for your buck touch that Trek always manages to figure out, just as Specialized often times does not unless you are willing to fork over another grand. The same can be said of the added carbon and Buzzkill components. They work and just add a little bit more to the smooth and comfortable ride.
On to the Sirrus Pro. First thing that you notice is the disc brakes. I have a rain bike hybrid with disc brakes. They are fantastic in the wet, no doubt. The rest of the time, they are psychotic overkill, especially in Dallas where it may never rain again anyway. And some of the worst injuries that I have ever seen to riders came from watching them face plant because of their disc brakes. The A1 Premium Aluminium frame with its FACT carbon seat stays and Zertz inserts are okay for a smooth ride, but I have a bike with that frame (I was out for a couple of hours on it today in fact) and there is no comparison between it and the Trek frame. The Trek technology is just that much better in terms of design quality and resulting performance, like in terms of responsiveness, quickness and stability. It even cuts the wind better than I ever thought that a hybrid would. The Trek carbon fork works. It is forgiving and compliments the rest of the bike well, especially in terms of handling. The Sirrus Pro's aero funk FACT carbon fork doesn't. It just doesn't work. It doesn't handle near as well, and even manages to be both sluggish in tight quarters, while also being way too twitchy and jiggy when cornering at speed. I never felt comfortable slicing a turn on the Sirrus Pro as a result. On the Trek, I routinely carve them, again a rare thing to find yourself doing on a hybrid. The combination Deore and Ultegra drivetrain that Specialized uses is nothing compared to the Ultegra/105 set up. It feels clunky, sluggish and mismatched to a point of being really noticable. The last straw for me was the wheelset. (And that was compared to the Select set that I got. This would be even more psychotically true compared to the Race set on your 06.) The Alex AT-400 wheels are stupid heavy and slow. When combined with the Nimbus Armadillos, which have the rolling resistance of a tank tread, they make you work a whole lot harder than they ever should. Riding the Sirrus Pro feels like you are chugging along on a 30 pound hybrid. (I know. I have one for my rain commuter. All I can say is ugh. What a frikkin beating.) The wheels are crap too, and have resulted in a whole lot of returns and nasty encounters in the shop portion of my local Specialized dealer. You see that backed up in posts to forums like these too. I don't know why Specialized puts such crap wheels and tires on some of their bikes, but they do. Even the R600's that they put on the LTD are nothing special, and are certainly no comparison to the Race wheels that Trek will be giving you, without charging another $800 to boot.
There are other little things that you notice when you use these bikes too. The Trek guys design the cable paths so that you can put a bike in a rack and not have it resting on the cables and scratching the bejeezus out of your nice new frame. Specialized routes theirs along the bottom of the top tube, with the cable fittings right smack where they will conflict when the bike is in a rack. Trek even does a better job of designing in cleaner cable routings and set up. Look at pictures of the the two bikes to compare. Which do you think looks cleaner and better fit? Trek gives you a really nice crankset. Specialized uses a chunky version that looks cool in black but does not nearly perform as well, like out on a climb or in a power start to shoot across a busy road. Those dead zone cranks, combined with a clunky drivetrain, lead wheels and rear tractor tire tires are not nearly as fun to take out on the road, much less to take across a busy one under precarious conditions.
But hey, opinions vary of course. I say give them both a hard look and see what you think. As for me, I couldn't be more pleased with my purchase, and would be really missing out on a lot if I had gone with the Sirrus Pro. Hope this helps!