Yes and no.
Before you deleted the .htaccess, the server was complaining that you can't run the statements in the .htaccess file, so the whole thing was bombing.
Now without that file, the server is telling you that it can't find the files you are linking to. The missing .htaccess file is *not* the problem. You're links are simply pointed to files that don't exist, at least not in the place the server is looking.
The statements in the (now deleted) .htaccess file would have caught the error of the missing files and re-directed to the home page so your website wouldn't look broken (like it is now).
Hope this helps...