I'm not the first person to suggest that Lost's opening plane crash is reminiscent of the 9/11 attacks, so you may find you've considered some of the following similaries already. If so, that's great, because you're on the right track.
The most important thing to note about the crash is that it doesn't symbolize America itself being attacked, but rather America's image being attacked. "Oceanic" isn't a place -- it's a brand, a corporate identity. In that same way, the Oceanic flight doesn't represents America but America's image, the way it appears both to itself and to others.
Before the crash, the Oceanic brand represented comfort and safety in the air, just as, before the 9/11 attacks, the "America" brand represented comfort and safety. The passengers (most of them, at least) took the Oceanic brand as an assurance that the flight would remain airborne, just as most Americans took the "America" brand as an assurance that their country would remain high-flying. When the crash ruins Oceanic's safety record, Oceanic's image -- a red, white, and blue logo of spots and swirls -- literally comes crashing down to earth. Similarly, when the 9/11 attacks ruined America's record of safety, America's image -- a red, white, and blue logo of stars and stripes -- came metaphorically crashing down to earth. America itself wasn't destroyed by the attacks, but its image was.
We see this idea revisited later, when the castaways return to the mainland and hold press conferences designed to repair Oceanic's damaged image. We also see it in the castaways new choice of carrier, Ajira Airways. Whereas the Oceanic branding was gentle and serene, the Ajira branding is dynamic and aggressive. This change in branding reflects America's change in image after the 9/11 attacks. Whereas America had previously held an image of comfort and serenity (Oceanic's soothing circles), America's actions in the War on Terror caused that image to become one of fiery aggression and interventionism (Ajira's fiery, pouncing tiger).
To get you started, I've made a list of a few ways the crash on September 22 resembles the attacks on September 11. For the sake of clairity, I've left out character information and just focussed on the crash itself.
By the way, if you're wondering why the crash seems accidental but the 9/11 attacks were deliberate, fear not -- in this final season, Lost should be tidying up some loose ends regarding the cause of the crash. (If you ask me, the pilot flew there on purpose, in the style of a 9/11 hijacker, given his insistence that everything was alright after the crash, as well as his willingness to "martyr" himself to the monster. But of course, I could be wrong.)
Some ways that the crash is like the 9/11 attacks
On Lost, the crash occurs on September 22. In real-life, the attacks occurred on September 11. (Think of Lost's date as "September 11, version 2".)
The crash on Lost involved a downed plane. The real attacks involved downed planes.
Previous feelings of safety
Before the crash on Lost, most of the passengers felt safe, believing that the plane was high-flying and in no danger of crashing. Before the 9/11 attacks, most Americans felt safe, believing in America's image as a high-flying nation with no danger of being attacked.
Being brought down to earth
The crash brings the plane down to earth. The 9/11 attacks brought America's image down to earth.
The chaos doesn't end with the crash, as the burning wreckage of the fuselage still poses a danger. The 9/11 attacks didn't end with the plane crashes, as the burning wreckage of the towers still posed a danger.
On Lost, there is a towering wing that threatens to collapse. In real-life, there were two towers that threatened to collapse.
On Lost, burning jet-fuel causes both the engine and towering wing to explode. In the real-world, burning jet-fuel caused both the towers to collapse.
After the explosions, Hurley's face is covered in white sand. After the collapse of the towers, the survivors' faces were covered in white ash.