This is actually much simpler than it looks. If the noun is singular, we use 'is' and if the noun is plural we use 'are' - it's as simple as that. 'Transport' is a singular noun (no 's' on the end) - There is a lot of transport. This is the same for any uncountable noun: There is a lot of money. There is a lot of noise. There is a lot of food. There is a lot of time. All of these words are grammatically singular, so the verb is singular. 'Books' is plural, so we say 'There are a lot of'.

There is a lot of transport but there \are a lot of books