"Unorganised" would imply that it is not at all organised, which is probably not true - transport networks have a great deal of structure and organisation. You appear to be making a comment on the quality of its organisation rather than a complete absence of it.
What I think you mean to say is that it is 'disorganised', meaning "badly planned and without order". You could also say it is 'badly organised', 'poorly run', or perhaps 'mismanaged'.