Nothing wrong with using .htaccess normally. There are a number of
reasons why we prefer to use the 404 script, but it sort of depends on
the number of redirects.

With thousands of changes, .htaccess gets a little bulky, for one,
unless you're in a position to do something a little more elegant with
regular expressions (e.g. everything moved from /default/ to / and the
file type  changed from .cfm to .php). Although, this can also get a
bit dicey. Rand ran into some trouble with "wildcard" redirects when
he moved from socengine  to seomoz.

The more complex the move, the more reasons to go with something other
than a list in .htaccess. With a script, you can set cookies, for
example if you're changing affiliate URLs at the same time.

Even if you don't use a 404 error script for redirection, I hope
everyone is watching those 404 errors for link recovery opportunities.
The more natural links you have, the more "typos" are going to happen
in those URLs. If you can spot them, you can redirect and keep the
traffic and link.

Dan