Because the (second) real Mr Rochester had been tragically in love with a girl called Jane. She died in his arms, before he could obtain a divorce from his unconsummated 'paper' marriage to a harlot. Before she died, Jane begged (this) 'Mr Rochester' (first name George) not to hesitate to fall in love again. Years later, 'Mr' (George) 'Rochester' did - with Charlotte. Hence the name 'Jane'; a tribute to 'Mr' (George) 'Rochester's first true love.
Eyre is an ancient word meaning 'circuit court'. Giving her character this surname was symbolic for Charlotte - it shows that "Jane Eyre" is, in essence, about justice.