The Long Answer:
Intelligent design theory is often controversial because it claims that aspects of the natural world are the result of intelligent action rather than naturally occurring chance, or law-governed processes. For example, the scientific theory currently dominating scientific thought regarding the origin of biological organisms is the highly regarded theory of evolution, which offers chance-law-governed mechanisms (mutation and selection) to explain observed characteristics of life. Intelligent design theory claims that at least some aspects of the biological realm are the result of intelligent action, rather than a chance or law-governed processes, such as the mutation-selection mechanism thought to be driving evolution. By proposing intelligent cause over mechanistic cause, intelligent design theory presents a competing hypothesis to the highly regarded dominant evolutionary paradigm of biological origins, and thus often finds itself facing much opposition from the scientific community.
Intelligent design theory is also controversial because it possibly (though not necessarily) implies that non-mechanistic causes were involved in the origins and history of life on this planet. This presents a potential challenge to both the methodological naturalism of those who practice science and also to the philosophical naturalism held to be true by many scientists. While intelligent design theory does not necessarily imply that any intelligent causes were non-natural or supernatural, the possible philosophical implications of the existence of an intelligent designer challenges the worldviews and metaphysics of many. This is often an unidentified, unrecognized, unrealized, or unadmitted source of opposition to intelligent design theory. As far as the methods of science are concerned, popular philosophies of science employ methodological naturalism which says that thinking about or seriously discussing the possibility of non-natural explanatory causes for the natural world are taboo--regardless of whether or not the past action of these non-natural causes is testable or identifiable! Thus intelligent design theory presents a potential challenge not only to the way scientists operates (methodological naturalism), but also to the worldviews of many scientists (recognized or unrecognized philosophical naturalists). Combined in varying degrees, these two components are what really drive much of the opposition to intelligent design theory.
Much of this opposition is expressed as Thomas Kuhn's "paradigm opposition" which he describes in his book The Structure of Scientific Revolutions:
Predictably, intelligent design theorists have experienced that journals have resisted publishing data which supports intelligent design theory or challenges evolutionary theory. Those who espouse design are explicitly or implicitly marginalized in the scientific community. This form of collective peer-pressure /social opposition to intelligent design theory which keeps many scientists from considering design also makes intelligent design theory controversial.
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