Side by side code sample for removing index.php with web.config instead of .htaccess
Hopefully seeing it side by side can help make the connection.
web.config
<?xml version="1.0" encoding="UTF-8"?>
<configuration>
<system.webServer>
<rewrite>
<rules>
<rule name="Index.php" stopProcessing="true">
<match url="^site/?(.*)$" ignoreCase="false" />
<conditions logicalGrouping="MatchAll">
<add input="{THE_REQUEST}" pattern="^POST" ignoreCase="false" negate="true" />
</conditions>
<action type="Redirect" url="/{R:1}" redirectType="Permanent" />
</rule>
<rule name="File exception" stopProcessing="true">
<match url="^(.*)$" ignoreCase="false" />
<conditions logicalGrouping="MatchAll">
<add input="{REQUEST_FILENAME}" matchType="IsFile" ignoreCase="false" negate="true" />
</conditions>
<action type="Rewrite" url="/index.php/{R:1}" />
</rule>
</rules>
</rewrite>
</system.webServer>
</configuration>
.htaccess
RewriteCond %{THE_REQUEST} !^POST
RewriteRule ^site/?(.*)$ /$1 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/$1 [L]