First of all, let me say that all of the above posters who wonder "what the big deal is of a laser hitting the bottom of a plane when the cockpit window is on top" are uninformed. As a pilot on final approach, the only direction I cannot see is directly behind or directly under me, but I continuously scan every other segment of the sky. Especially at night I have to let my eyes pause for a moment on each section in order to discern relative motion, as a quick scan would not allow me to detect the characteristic red/green/white nav lights + strobe of a moving aircraft above the many lights (both stationary of all color, flashing, and more slowly moving ground vehicle) below the aircraft. So a fair amount of our time on final approach is spent gazing downward, since while descending that part of the sky represents the largest risk of collision hazard. This attentive watchfulness is of course an important part of what we do, and if while looking for aircraft below us both pilots are "temporarily blinded" or worse (depending on the type of laser used) we are obviously in a very scary situation.
Secondly, this idea that pilots fly the approach on autopilot is misinformed. Yes, cruise flight and the initial segment of the approach are usually (but by no means always) performed with the assistance of an autopilot. However, the autopilot is routinely and often given manual commands in a terminal environment to comply with air traffic control instructions all the way up to the very last final intercept of the glideslope. So pilot incapacitation during any descending maneuver before that final segment poses a very real threat to people on the ground below the aircraft's path (a much larger area than the airport proper). Also, with the exception of some large airliners and very few corporate aircraft, most jets do not have autopilots approved for autolandings, so at some point during the last 200 to 1000 feet the pilot will hand fly the plane, adjusting the pitch attitude and simultaneously reducing thrust to make a smooth landing flare. This is not something I want to feel my way through without sight.
There are many reasons to not use autopilot, some flights are also operational line checks where the pilot in command is being evaluated by a check airman who expects them to hand fly the plane to demonstrate proficiency. I often fly by hand both to keep my skills sharp as well as because it is enjoyable to have the responsiveness of a very powerful jet airplane at my fingers. There is satisfaction in rolling the plane onto a perfectly aligned final approach without the autopilot's assistance.
As a group, professional pilot's take the safety of our passengers very seriously. We attend recurrent training continuously throughout our careers, and simulate almost every conceivable emergency that it is possible to contend with. However, some emergencies elude constructing nice pat standard operating procedures to deal with. Obviously if an aircraft comes apart in flight then all you can do is follow the arc of the individual parts toward the ground below. Likewise, becoming blind is a situation that we just can't train for.
Finally, I've also noticed some posts recommending using some sort of film on the windshield that would protect the pilots. This is unlikely to happen soon for several reasons. I would love to hear that such a material exists that is effective over the many frequency ranges that could conceivably be used in a laser. But even if it did exist, each aircraft has a slightly different type of construction and would require a huge amount of research and development. The price would be astronomical. As an example, the windshield of a Learjet is nearly an inch thick, is comprised of multiple layers of various materials (including different types of plastic and acrylic and a layer of gold used to heat the windshield) which have been thoroughly tested for strength, compatibility, temperature and impact tolerance among other things. One segment costs nearly $100,000 installed. I also noticed someone mentioning polarized lenses. It is recommended that pilots not use polarized glasses because when you look at the windshield through them there are glaring distortions and areas that are difficult to see through because of the many layers and material types used in the construction of the windshield. Use of such lenses could inhibit a pilot's ability to see and avoid other traffic and so constitute a safety hazard.
I hope that someone will develop an effective and not too costly lens that could be worn like regular glasses and not interfere with colors, night vision, and the many material types used in aircraft windshields. But in the meantime I wish law enforcement the best in pursuing every criminal who threatens public safety with lasers - whether negligently, with terrorist intent, or through incredible stupidity. Will deterrence be enough? Of course not. But I believe it will have some effect -- even one accident prevented would be a Good Thing. It should certainly be a starting point, hopefully many will take heed so that law enforcement can focus their attention on the truly malicious.
Note: I am NOT concerned about the $15 consumer lasers mentioned in the USA Today article but about the much stronger lab types, so please don't waste your time explaining to me why I shouldn't be at all worried about this.