What are the reasons for journals to have a policy against publishing material available as a preprint?
A a chemist, I'm very well aware of this. 

Here's the ACS Journal Editors' Policy on Preprints' point of view about the disadvantages of preprint servers:


  The disadvantages of preprint servers include: the potential for flooding the literature with trivial and repetitious publications, thus making extraction of reliable and valuable information more difficult; absence of peer review; possible premature disclosure with inadequate experimental details or supporting data; premature claims of priority; potential lack of proper references and credit to prior work; abuse of multiple revisions or updates; possible lack of duration and long term archiving.


Personally, I find the two concerns about 


"premature claims of priority" and 
"abuse of multiple revisions or updates" 


the most relevant points. 


"flooding literature with trivial publications" is IMHO an issue with and without preprint servers, 
"repetitious publications" for me fall into the same category, as do
"inadequate experimental details or supporting data".
"absence of peer review" is clearly visible with papers from preprint servers - which is IMHO an advantage over journals where the peer review is uncritical.
"long term archiving" depends IMHO more on the responsible organization behind the server (I'm not any more concerned that arXiv could shut down than e.g. Langmuir, Analyst or Analytical and Bioanalytical Chemistry)


There have been "experiments" with preprint servers for chemistry some 10 years ago [1] but AFAIK they did not develop the momentum e.g. arXiv has, and they seem to have died meanwhile.
See also: Cecelia Brown: The Role of Electronic Preprints in Chemical
Communication: Analysis of Citation, Usage, and Acceptance in the Journal Literature, Journal of the American Society for Information Science and Technology 54.5 (2003): 362-371.
(the discussed server seems to be down - or at least I can't get a response).



Personal point of view on the problem

The possibility to be able to publish a manuscript on a preprint server before submitting it to a journal is not as imortant for me personally as the possibility to make the final contents of the paper publicly accessible. 

Thus I can live quite well with not being allowed to submit manuscripts that are already available on preprint servers as long as I'm allowed to also publish the manuscript (preferrably the final version after peer-review) after I submitted it to the journal.


either at a preprint server (arXiv), or
on institutional, personal or project web pages
(preferrably both, of course)