I have been fighting state departments of transportation for years about this. Same goes for tunnels. Kentucky, Tennessee, and the National Park Service built a multi-million $ 4-lane tunnel under Cumberland Gap - then the park closed the old road over the gap - tore out the roadbed - replaced it with a trail - and banned bicycles. They could care less about bicycles. You can bike up the expressway to the security window at the tunnel, hope to catch someone's attention, then wait until they can get you thru the tunnel. Of course, bikes are banned in the tunnel. They insist that it is a courtesy service. I tell tham that I should sue them over misuse of ISTEA multimodal funds.
Same goes for the Whittier Tunnel in Alaska. The government spends bazillions of dollars to move cars more quickly and actually makes it impossibile for cyclists to transit the mountain in question. The St. Francisville ferry in Lousiana - the last on the Mississippi between New Orleans and New Madrid - is set to end service when the big new bridge is finished. The new bridge is "supposed" to allow cyclists, but it will also include miles of expressway riding to access the crossing. Ughh! Ferries on large rivers are a thing of the past - but they are a great way to cross a river. You actually have to stop and acknowledge - "Hey, that is one big river."
There are still a couple of ferries on the Upper Mississippi - two in the St. Louis area - Grafton and, better yet, the Golden Eagle Ferry. South of Cairo, Illinois there is a ferry between Dorena, Missouri and Hickman, Kentucky - I took this years ago. More correctly - the ferry had been out of business for some time, but the owner took me across anyway. Amazing! It now has state support to provide a critical connection and is worth considering if you are riding in that area.
As for the TransAm crossing at Chester - the Popeye Bridge is narrow and dangerous. There is a beautiful new bridge with bike lanes at Cape Girardeau - or a ferry - yes a ferry - at Ste Genevieve. And Ste Genevieve is a lovely historic river community from French colonial days. If you can find ferry crossings of other big rivers - I'd suggest planning your route accordingly. The ferry crossings are so nice - plus cars tend to avoid these routes because they don't want to be delayed.