There is no "Connection Manager" that you can delete it (I can't find it). I found one way to delete old or faulty FTP connection (let's say it's 'connection123').
- Create new Web Project (or choose existing)
- Click right on 'Connections' and select 'Connection Manager'
- Click green '+' and change name for example 'Name1'; in 'Source' choose 'Project'; in 'Destination' choose 'Remote' and select connection (our 'connection123') that you want to modify or delete; Apply or OK
- Under 'Connection' in Project Explorer View our Connection appear ('connection123')
- Click right on 'connection123' and choose 'Delete'
IT'S DONE! ;-)