You don't pay a toll at inter-state crossings if you're a private vehicle. What I think you might have experienced are just the ridiculous number of toll booths setup on highways to collect fees for newly constructed sections of the highways. These road project contracts are handed over to external construction companies and they recover the costs by collecting toll for the next 10-15 years. A 5 hour journey from Bangalore -> Chennai includes 6-7 stops at toll booths each adding 5-10 mins to the journey depending on whether the cars before you have the exact change or not and how lazy the toll booth operator is.