Drexler's article is, in my opinon, simply inaccurate. The suffix -ism is used not only for political, ideological, and religious opinions, but also for philosophical opinions and theories in exact sciences and mathematics whose accuracy is a matter of dispute, or has historically been a matter of dispute. He's also displaying what appear to be strange gaps in his vocabulary -- Mendelism (alternatively Mendelianism) and Newtonianism have been widely used terms for centuries, as a simple search of Google Books will show.
In the concrete case of Darwinism, the term is very useful to differentiate Darwinian evolution from other theories of biological evolution that have been proposed historically, like Lamarckism or intelligent design.
Connotations don't study history or philosophy, what matters in the context of Drexler's article is prevalence in popular perception, and resulting normative recommendation.
I feel that the term "rationalism", as opposed to "rationality", or "study of rationality", has undesirable connotations. My concerns are presented well by Eric Drexler in the article For Darwin’s sake, reject "Darwin-ism" (and other pernicious terms):
So, my suggestion is to use "rationality" consistently and to avoid using "rationalism". Via similarity to "scientist" and "physicist", "rationalist" doesn't seem to have the same problem. Discuss.
(Typical usage on Less Wrong is this way already, 3720 Google results for "rationality" and 1210 for "rationalist", against 251 for "rationalism". I've made this post as a reference for when someone uses "rationalism".)