According to https://prestodb.github.io/docs/current/installation/jdbc.html you need to set a property: SSL=true
In FME 2018.0 or later you would do this by editing your Presto database connection to include a Connection Property "SSL" with a Value of "true". See the screenshot below.
Note 1: This advice is theoretical; it hasn't been tested with an actual Presto database.
Note 2: I see lots of other SSL related properties in the Presto doc; you might need to set some of them as well.
Note 3: In FME 2017 or earlier you can add "?SSL=true" to your connection string to achieve the same result. That will also work in 2018.0+, but the property solution is a bit easier to read.