The Doctor has been to Rome multiple times. Here is a list of stories;
- An unknown point before "An Unearthly Child" (mentioned in "Byzantium!" (BBC Past Doctor Adventures novel #44))
- "The Rescue", "Byzantium!" (BBC Past Doctor Adventures novel #44), and "The Romans" (these three count as the same time because he didn't leave Rome in between these stories)
- "The Indestructible Man" (BBC Past Doctor Adventures novel #69)
- "The Best of Days" (short story)
- "The Stone Rose" (BBC New Series Adventures novel #7)
- "The Fires of Pompeii"
- "The Pandorica Opens"/"The Big Bang"
- Off-screen at an unknown point before "The Impossible Astronaut" (referred to in "Day of the Moon")
So that's at least 8 times! However, speaking from an in-universe perspective, he could have visited Rome any number of times in adventures we didn't see.