Toy public/private key example open to frequency analysis?
The site also misrepresents RSA encryption. If you are using textbook RSA (i.e. this scheme, with no padding), you don't independently encrypt each letter. Rather, you take the entire message, treat it as a number, and encrypt that.

This doesn't work if your primes are 3 and 11, but if they're each, say, 8 bytes long, then you could encrypt a 16-byte message using textbook RSA by treating the whole message as a single number. The only time you run the encryption operation multiple times on different parts of the message is if the message is longer than the RSA modulus, in which case you need a chaining mode.

RSA has no real chaining modes (no one's bothered coming up with one), but a real block is fairly big anyway. The site broke the message into letters and encrypted each separately (which is the horrible no-good ECB mode) to make the math easier, but that's not even how textbook RSA is used.

There are all sorts of attacks on textbook RSA; frequency analysis isn't really one of them.