Jefferson, as great as he was--and he WAS great--lived in the 18th century and was talking about a new, fledgling nation that had just been created.
Roosevelt ran a 20th century national that was one of the larger ones on the planet, and thus one of the larger TARGETS on the planet, and as such, when you're a target, people will inevitably attack you, and so inevitably you then need and seek out friends to protect you, that's basic human nature, Hobbes went so far as to give that as a reason for creating a government--because in a State of Nature, all out for themselves, even the strongest person is susceptible to attack, hence HE seeks allies, hence the others do as well, and so we get Leviathan, a state that serves as essentially an "alliance" between 300 million people who agree not to attack each other and that if people in Hawaii are bombed folks from New York will come and help, and vice versa.
Jefferson wasn't wrong at all, not saying that.
But he made his statement in relation to a nation that was radically different from the one Roosevelt had, and the late 1700s-early 1800s was radically different, as far as what America was, than the 1900s.
In 1700 America is a dream.
In 1800 America is an infant, in no position to fight.
In 1900 America's come of age and must grow stronger, as TR saw and FDR later had to act upon.
And in 2000...
Well, sadly so far it's been a nightmare...but NOT because we've had allies--it's because we've abused them...remember the Trans-Atlantic Alliance? Remember when Europe and Canada didn't think we were arrogant scum?