Mint uses yodlee, a company that does account data services for many large banks and investment firms.
Obviously your account information is stored somewhere in a database. My point above was that mint itself isn't an avenue forgetting to log off at the internet cafe or having a key logger at the library while you use mint is going to expose you to financial damage, except maybe someone realizing you've got lots of money.
Sure, maybe someday a hacker can break into yodlee. Or your bank, or fidelity, or vanguard, or your email account with all those juicy electronic statements. But worrying about that sounds like my Mom, who still refuses to bank online because she's worried about security of it all. She's right technically I mean the bank's database is there to be broken into anyway but using the internet to manage her account does expose her to a little more risk.