From the script online:
I want to show you something, Ethan.
He now shoves the papers across the table. They're xeroxed
copies of a Wisconsin bank account in the name of DONALD and
MARGARET ETHAN HUNT. It shows a balance of $127, 000.
Since your father's death, your family's
farm has been in sub-chapter S and now,
suddenly, they're flush with over a
hundred and twenty grand in the bank.
Dad's illness was supposed to have wiped
out the bank account -- dying slowly in
America after all, can be a very
expensive proposition Ethan. So, why
don't we go quietly out of here onto the
So what appears to have raised the suspicion of IMF is that Ethan's father had died after a long illness and that his mother should have only had very little money in her bank account and the farm she owned with his father is bankrupt.
At no point is it implied that IMF think that this is the sole money that Ethan as the suspected mole in IMF has received. The NOC list that is at the center of the plot in the movie is worth millions.
The fact that Ethan's mother, a poor widow, suddenly has a large amount of money in her checking account is just a piece of evidence they are using along with the fact that Ethan was apparently the only agent to survive a botched mission. Yes, perhaps Ethan does earn enough money to be able to support his Mother - but enough to gift her over $120k? As far as IMF are concerned this piece evidence is suspicious and enough to want to detain Ethan for more questioning.
Later in the script:
..when you think about it, Ethan, it was
inevitable..no more Cold War. No more
secrets you keep from everyone but
yourself, operations you answer to no one
but yourself. Then one morning you wake
up and find out the President of the
United States is running the country -
without your permission. The son-of-a-
bitch! How dare he? You realize itís
over, youíre an obsolete piece of
hardware not worth upgrading, youíve got
a lousy marriage and sixty-two grand a
year. Kittridge, weíll go after that no
good son-of-a-bitch, big time!
So Phelps, Ethan's team-leader in IMF earns $62,000 a year, so it is likely that Ethan earns less than this. This is probably in line with a 'high end programmer' in 1996 - but one imagines that agents like Ethan (or James Bond or ... name any fictional spy) are probably not in this for the money, but they are somehow attracted to the danger, challenge and jet-setting lifestyle.