English Translation
Tom is the one who doesn’t understand.
The expression “Тому-то и непонятно” is a little idiomatic, so it helps to break it down.
тому — “to that person” / “for that person”
-то — an emphatic particle (“that’s exactly…”)
и — here means something like “that’s precisely why” or “indeed”
непонятно — “it is unclear,” “it doesn’t make sense”
So the overall meaning is:
“That’s exactly what they don’t understand.”
“That’s precisely what’s unclear to them.”
“That’s the very thing they don’t understand.”
“That’s why they’re confused.” (depending on context)
For example:
— Почему он не пришёл?
— Тому-то и непонятно.
Literally:
“Why didn’t he come?”
“That’s exactly what isn’t understood.”
Natural English:
“That’s the mystery.”
“That’s exactly what nobody understands.”
“That’s what we’re trying to figure out.”
The combination X-то и Y is quite common in Russian and often has the sense of “that’s exactly the point”:
Вот-то и дело. — “That’s exactly the point.”
В том-то и проблема. — “That’s exactly the problem.”
В том-то и беда. — “That’s the trouble.”
Тому-то и непонятно. — “That’s exactly what they don’t understand.”