0:05 ~ 0:09
Suzume's hometown appears to be very loosely based on Nichinan, Miyazaki, with Aburatsu Port being a close match to the port from the movie. Actual locations don't seem to exist though, the similarity is mostly the landscape looking at the port, and there's no ferry to Ehime.

31° 34′ 55″ N, 131° 24′ 14″ E

0:09 ~ 0:10
Yawatahama Port, Ehime. The building appears to have been demolished at the time of writing.

33° 27′ 26″ N, 132° 25′ 7″ E

0:10 ~ 0:12
Scenery roughly (and the bridge shown in the movie definitly) matches this road along Oya Pond, Ehime.
Credits for finding: http://tsurebashi.blog123.fc2.com/blog-entry-522.html

33° 53′ 16″ N, 133° 5′ 55″ E

0:12 ~ 0:13
Supposedly Suzume is in Ehime, but the bus sign as shown in the movie (and somewhat visible here), matches the sign used at the Taketazu Port in Kunisaki, Oita prefecture as shown on this Wikipedia image: https://commons.wikimedia.org/wiki/File:Bus_Stop.Taketazu_Port.jpg. Specifically, their old design as shown on Wikipedia and here (33° 40′ 33″ N, 131° 35′ 28″ E). There appear to be 2 versions, one with English text, which was used in the movie, and one with the Japanese text "バスのりば", which still just means bus stop.

0:14 ~ 0:15
This is Anywhere, Rural-ish Japan.

0:15 ~ 0:17
I looked in Ehime, this one vaguely resembles it except for the background and McDonald's pole.
"Himawa-" is visible through the window at 0:18 ~ 0:19, which may be a hint, but who knows.

33° 48′ 10″ N, 132° 46′ 58″ E