That depends on when/where they're getting flagged as spam.
The first level of spam filtering happens at the server side, where Apple's Mail servers (assuming you're using an iCloud email address) categorize mail based on a set of rules around common spam sources, untrusted domains, incorrectly signed messages, etc. They are filtered before your system sees it.
The second level happens on your system, where you have some control over it. The first run would be to add a Mail Rule (Mail -> Settings -> Rules -> Add Rule) that looks something like:

Here you can see the conditions to match (i.e. From contains 'example.com').
For any match the message is moved to your Inbox and Mail stops processing rules (this should prevent any subsequent filters from moving the message somewhere else.
If the rule doesn't work, you'll need to look at the message headers (Mail -> View -> Message -> All Headers) to see if you can figure out why. If it's a problem with the domain the emails are coming from, then the problem may be outside your control and you'll need to talk to the domain owner about fixing their setup.