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I can think of two reasons just off the top of my head.
1. Not everybody is running Apache servers, and setting Friendly URLs without having the appropriate server rewrite rules causes Bad Things to happen.
2. Some hosting providers use the .htaccess file to set certain required features, like the location of the php.ini for for the desired version of PHP. Installing your own .htaccess file will overwrite that, again causing Bad Things to happen.
The reason it's not part of a default MODX installation is that whether or not the site even uses an .htaccess file or what Apache configuration is done in any such .htaccess file is highly variable, depending on the hosting server's configuration.
You could provide a form that will appear during the install that has checkboxes for those options and explains when, and when not, to select them.
You can also test for Apache with isset('DOCUMENT_ROOT'), since I think Apache is the only platform that sets it.
[ed. note: BobRay last edited this post 10 years, 9 months ago.]
I am also try this way to seo friendly url