Reading up on it on wiki my understanding is that the rule had been if the winning CL team didn't qualify for the competition the national FA could decided to give the winners, in this case Liverpool, the fourth spot instead of Everton. The FA had previously had said in 2003/4 that if Arsenal or Cheslea won the Champions League they would get the fourth spot. But then decided that from then on only the top four teams would get the spot but when Liverpool ended up winning the Champions League that came back to bite them. So really, the English FA made a bit of a cock and UEFA had to change the rules accordingly.
Which is the way it should be, if you win the competition, you should be qualified for the competition the next year. That was historically how it worked (which is why if you search through old European Cup and early Champions League seasons you'll see occasions when two clubs from the same league competed ie. Liverpool and Nottingham Forrest who actually played each other in the 78/79 European Cup).