In most of cases, .htaccess file is hacked for malicious redirects.
There may be some conditional redirect, you can execute rewrite rule if referring page contains google, yahoo or msn.
Sometime Google search shows this site may be hacked, this is because hacker hacked the website or have made some changes in existing pages on the site.
If you will get malware warning on your website or it is redirecting to malicious site then first investigate your .htaccess file manually.
You will see some similar conditional redirect like this :
RewriteEngine On
RewriteCond %{ENV:REDIRECT_STATUS} 200
RewriteRule ^ - [L]
RewriteCond %{HTTP_USER_AGENT} (google|yahoo|msn|aol|bing) [OR]
RewriteCond %{HTTP_REFERER} (google|yahoo|msn|aol|bing)
RewriteRule ^(.*)$ ????.php?$1 [L]