There are many journals that do not accept, or actively discourage LaTeX-based submissions. I've always found the assumption in LaTeX heavy fields that it's ubiquitous to be an interesting quirk.
For example, two journals that will accept LaTeX based submissions, but would rather you not:
American Journal of Epidemiology:
Prepare your manuscript, including tables, using a word processing
program and save it as a .doc, .rtf or .ps file. All files in these
formats will be converted to .pdf format upon submission. Please note:
This journal does not accept Microsoft Word 2007 documents at this
time. Please use Word's "Save As" option to save your document as an
older (.doc) file type.
Prepare any other files that are to be submitted for review, including
any supplementary material. The permitted formats for these files are
the same as for manuscripts and figures. Other file types, such as
Microsoft Excel spreadsheets and Powerpoint presentations may be
uploaded and will be converted to .pdf format. It is also possible to
upload LaTeX files but these will not be automatically converted to
.pdf format (and are therefore discouraged). The journal staff,
editors and reviewers will only be able to view these unconverted
files if they have the appropriate software, which cannot be
Manuscripts should be in a standard word processing format. We prefer Microsoft Word but we can also use RTF, TXT, LaTeX2e, and AMSTex. Application software programs released before 2001 are not supported.
The New England Journal of Medicine actively doesn't accept them, at least not unless converted to a PDF:
All text, references, figure legends, and tables should be in one
double-spaced electronic document (preferably a Word Doc). You may
either insert figures in the text file or upload your figures
separately. We prefer the former, but this may not work well for
complicated graphics, which should be sent separately. It is
permissible to send low-resolution images for peer review, although we
may ask for high-resolution files at a later stage.
Legends for all figures should be included in the file with the text
and should not appear on the figures.
Our preferred file type for new manuscript submissions is a Word or
text document with all figures in the same document. We will also
accept Adobe Acrobat portable document format (.pdf) , WordPerfect
(.wpd), text (.txt) documents, or .rtf file format.
Clinical Infectious Diseases doesn't even want your PDFs:
The preferred format for submitting manuscripts online is Microsoft
Word (.doc files). PDF files are not acceptable for submission.
These are all very good journals in my field - a happy, healty, high-impact, tenure friendly career could very easily be had never touching LaTeX.