Ho avuto anche lo stesso problema,
Quello che ho fatto è stato rinominare il .htaccess sia nella directory principale che nella directory / pub. ha risolto il mio problema.
Inoltre, puoi sostituire .htaccess con questo
############################################
## uncomment the line below to enable developer mode
# SetEnv MAGE_MODE developer
############################################
## uncomment these lines for CGI mode
## make sure to specify the correct cgi php binary file name
## it might be /cgi-bin/php-cgi
# Action php5-cgi /cgi-bin/php5-cgi
# AddHandler php5-cgi .php
############################################
## GoDaddy specific options
# Options -MultiViews
## you might also need to add this line to php.ini
## cgi.fix_pathinfo = 1
## if it still doesn't work, rename php.ini to php5.ini
############################################
## this line is specific for 1and1 hosting
#AddType x-mapp-php5 .php
#AddHandler x-mapp-php5 .php
############################################
## default index file
DirectoryIndex index.php
<IfModule mod_php5.c>
############################################
## adjust memory limit
php_value memory_limit 768M
php_value max_execution_time 18000
############################################
## disable automatic session start
## before autoload was initialized
php_flag session.auto_start off
############################################
## enable resulting html compression
#php_flag zlib.output_compression on
###########################################
## disable user agent verification to not break multiple image upload
php_flag suhosin.session.cryptua off
</IfModule>
<IfModule mod_security.c>
###########################################
## disable POST processing to not break multiple image upload
SecFilterEngine Off
SecFilterScanPOST Off
</IfModule>
<IfModule mod_deflate.c>
############################################
## enable apache served files compression
## http://developer.yahoo.com/performance/rules.html#gzip
# Insert filter on all content
###SetOutputFilter DEFLATE
# Insert filter on selected content types only
#AddOutputFilterByType DEFLATE text/html text/plain text/xml text/css text/javascript
# Netscape 4.x has some problems...
#BrowserMatch ^Mozilla/4 gzip-only-text/html
# Netscape 4.06-4.08 have some more problems
#BrowserMatch ^Mozilla/4\.0[678] no-gzip
# MSIE masquerades as Netscape, but it is fine
#BrowserMatch \bMSIE !no-gzip !gzip-only-text/html
# Don't compress images
#SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
# Make sure proxies don't deliver the wrong content
#Header append Vary User-Agent env=!dont-vary
</IfModule>
<IfModule mod_ssl.c>
############################################
## make HTTPS env vars available for CGI mode
SSLOptions StdEnvVars
</IfModule>
<IfModule mod_rewrite.c>
############################################
## enable rewrites
Options +FollowSymLinks
RewriteEngine on
############################################
## you can put here your magento root folder
## path relative to web root
#RewriteBase /magento/
############################################
## workaround for HTTP authorization
## in CGI environment
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
############################################
## TRACE and TRACK HTTP methods disabled to prevent XSS attacks
RewriteCond %{REQUEST_METHOD} ^TRAC[EK]
RewriteRule .* - [L,R=405]
############################################
## redirect for mobile user agents
#RewriteCond %{REQUEST_URI} !^/mobiledirectoryhere/.*$
#RewriteCond %{HTTP_USER_AGENT} "android|blackberry|ipad|iphone|ipod|iemobile|opera mobile|palmos|webos|googlebot-mobile" [NC]
#RewriteRule ^(.*)$ /mobiledirectoryhere/ [L,R=302]
############################################
## never rewrite for existing files, directories and links
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l
############################################
## rewrite everything else to index.php
RewriteRule .* index.php [L]
</IfModule>
############################################
## Prevent character encoding issues from server overrides
## If you still have problems, use the second line instead
AddDefaultCharset Off
#AddDefaultCharset UTF-8
<IfModule mod_expires.c>
############################################
## Add default Expires header
## http://developer.yahoo.com/performance/rules.html#expires
ExpiresDefault "access plus 1 year"
ExpiresByType text/html A0
ExpiresByType text/plain A0
</IfModule>
###########################################
## Deny access to root files to hide sensitive application information
RedirectMatch 404 /\.git
<Files composer.json>
order allow,deny
deny from all
</Files>
<Files composer.lock>
order allow,deny
deny from all
</Files>
<Files .gitignore>
order allow,deny
deny from all
</Files>
<Files .htaccess>
order allow,deny
deny from all
</Files>
<Files .htaccess.sample>
order allow,deny
deny from all
</Files>
<Files .php_cs>
order allow,deny
deny from all
</Files>
<Files .travis.yml>
order allow,deny
deny from all
</Files>
<Files CHANGELOG.md>
order allow,deny
deny from all
</Files>
<Files CONTRIBUTING.md>
order allow,deny
deny from all
</Files>
<Files CONTRIBUTOR_LICENSE_AGREEMENT.html>
order allow,deny
deny from all
</Files>
<Files COPYING.txt>
order allow,deny
deny from all
</Files>
<Files Gruntfile.js>
order allow,deny
deny from all
</Files>
<Files LICENSE.txt>
order allow,deny
deny from all
</Files>
<Files LICENSE_AFL.txt>
order allow,deny
deny from all
</Files>
<Files nginx.conf.sample>
order allow,deny
deny from all
</Files>
<Files package.json>
order allow,deny
deny from all
</Files>
<Files php.ini.sample>
order allow,deny
deny from all
</Files>
<Files README.md>
order allow,deny
deny from all
</Files>
################################
## If running in cluster environment, uncomment this
## http://developer.yahoo.com/performance/rules.html#etags
#FileETag none
