Well, I'm just speculating idly of course, and yes, there's no sound reason to start suspecting anything more sophisticated than a substitution cipher yet, but cryptography was reasonably topical then. People used ciphers to conceal messages they had to send via telegraph (having to watch someone read and tap out a private message of yours mustn't be pleasant) and to encrypt messages put in personals sections of newspapers. Things like Poe's contest in Philadelphia and the Beale Papers apparently caused a public stir.

The reason I suggest a homophonic cipher (or similar) rather than something like the much more secure Vignere in use for telegraph messages (only recently broken for the time) is because the Vignere system is more complicated, and requires more working out than I would expect someone writing a private message to tolerate.

Homophonic systems, on the other hand, are fairly easy to invent and remember on a personal basis, and can offer some security against amateur analysis. Though the technique for solving them was known, they could still prove robust - the partially homophonic cipher of Lous XIV was still unbroken at this point, despite being over a century old.

I'm very much an amateur (though I have read that book) but it doesn't seem that ridiculous to suggest a homophonic cipher. At any rate, It's only something to consider if it turns out to be something more complex than a simple substitution cipher.

I highly agree with linguist on this point. It's very unlikely a homophonic substitution was used here. It's more complicated than you'd think. A great read on the subject can be found here: http://www.amazon.com/Code-Book-Science-Secrecy-Cryptography... if anyone's interested in learning more about cryptography. Very interesting.