First check that it is not your fault in using . htaccess, for example, does your server use Apache itself or use another as Ngnix.
Also check that it is in the correct folder or if there is no other folder.
I can’t believe you forgot to turn on the module, because if it was, it would have happened 500 internal error server.
There’s one thing that seems wrong in your rewrite:
You used /transportadora... when the right one would be transportadora..., at least this seems to me the most correct:
RewriteEngine On
RewriteRule ^([^/]*)/([^/]*)$ transportadora/cotacoesEnviaPropostaAceitarRecusar.php?acao=$1&id=$2 [L]
However rewrite is accepting any action and any id, which is strange, maybe one should try this:
RewriteEngine On
RewriteRule ^(recusa|aceita)/(\d+)$ transportadora/cotacoesEnviaPropostaAceitarRecusar.php?acao=$1&id=$2 [L]
- The 
(recusa|aceita) will only accept pre-defined actions. 
- The 
\d+ only accept numbers. 
							
							
						 
Have you checked whether apache rewrite mode is active? What is the error? puts the error print on the question to help answer.
– Miguel Batista
Try this http://pastebin.com/BNhp6Ts5
– Edilson