Yes, for me too.
I've just uploaded a project with Netbeans and it took 4:47 minutes. I've done the same with FileZilla and it took 1:48 minutes.
I think it's because it dones many other operations. For example, uploading the same file:
Netbeans:
...
RNFR forms.php
RNTO forms.php.old
Rename successful.
RNFR forms.php.new
RNTO forms.php
Rename successful.
DELE formus.php.old
File delete OK.
...
Filezilla:
...
Command: put "P:\Projects\...\forms.php" "forms.php"
State: Successfully transfered, transfered 4.096 bytes in 1 seconds
...
They should let us configuring this behavior.