Computers are just a tool. You can infer the sequence of a gene in a common ancestor without them; it just takes longer. But it's a useful demonstration of the technique, whose logic is transparent and difficult to refute. I taught a class of freshmen to do it a couple of years back.
Of course they were neither stupid nor irremediably prejudiced against the idea. Either would make it very hard to learn.
It is the presuppositions that are built into the program that I question. Once those are hardwired, no one questions them... they just look at the output and say it was "computer generated" and scientific.
Take a look at the Editorial in today's WSJ called, Climate of Fear. It takes this same issue out of the emotional (around here) context of evolution and clearly demonstrates it in the context of global warming - which also uses computers.
Further, it shows how a belief system can go out in search of proof - seeing "facts" through "global warming colored glasses" - and criticizing any disagreement by anyone who questions the underlying assumptions.
I urge everyone who has an interest in these types of issues to read this editorial. The author, Dr. Richard Lindzen, is a professor at MIT. Note especially the climate of fear that has been created by "objective" scientists against any scientist who dares question the same set of data and see a different rubric. How funding is withheld from those who see data differently. How academic promotions are withheld. In short, how everyone in an entire department can end up believing the same thing and advocating the same thing - even if it is not proven or simply not true. And yet at the same time, they can do all this under the guise of "science". It is a way to stifle all dissent and independent thought. And it happens every day in most fields of endeavor.
Scientists are simply humans - subject to all the emotional vaguaries of all humans.
Don't think for a moment that everything described by Dr. Lindzen doesn't equally apply to those humans who work with biological data and devote themselves to proving evolution.