Let's be a tad more accurate: thank you Clinton for not noticing that the Cold War was over.
The reason why there weren't enough armed fighters on alert to cover the country is simple in concept, but difficult to understand in practice.
Maintaining armed aircraft on constant alert is hard on aircrews, hard on aircraft, and leads to the occasional weapons mishap--and is thus very expensive over the long haul. To avoid these problems, the Pentagon, way back in the mists of the Cold War, "de-alerted" interceptors unless Soviet bombers were moved from operating bases deep inside the USSR (from whence they could not attack America) to forward bases in Siberia.
This made sense back in the days when the US and the USSR were engaged in the Cold War. However, the Cold War ended in 1991, and the Russian bombers began to cheerfully rust away at their main bases deep inside the XUSSR. We proceeded to de-alert our birds, and with only one exception (during the Kosovo mess in 1999), both sides stayed at low alert levels.
Nobody ever called the practice into question, even after Operation Bojinka was exposed in 1995. That's where those with at least the good sense God gave a crabapple should have started asking, "Why are we doing things like this?"