No, mod_rewrite is not basically just cloaking. Not sure where you got that idea.
Mod_rewrite rewrites a given url to something else, often for example changing a url that looks nice and friendly:
/folder2/subfolder4/file12.htm to say site.php?folder=2&subfolder=4&file=12
for example. This isn't cloaking, it's just creating a nicer looking url that gets spidered better in general since each programmed page appears to be a static separate url.
Other uses are assigning 301s or 302s to pages, for example if you rewrite a site, with proper rules the search engines, old backlinks, etc, will be correctly redirected to the new url transparently.
Cloaking is completely different, it queries either the user agent, to test if it's a spider bot, or the requesting IP address, to see if it comes from a certain IP range known to be used by search engine spiders, then delivers different content based on the results, spammy keyword stuffed content to the bot usually with IP cloaking, trimming of extra page content often for useragent based cloaking, which isn't really black hat at all, many of the biggest sites on the web use useragent based page alterations.
This process doesn't really involve any rewriting at all, it's usually done post http request, by the script engines of the site.
Modrewrite happens at the time the request is received by the server, before the request is processed by the site.
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