usando metodo sync

class Funcao extends Model
{
    protected $table = 'funcao';
    protected $primaryKey = 'id';
    protected $fillable = ['id','url','nome'];
    public $timestamps = false;

    public function areas()
    {
        return $this->belongsToMany(area_atuacao::class,'fun_area','fun_id','area_id')
            ->as('fun_area')
            ->withPivot(['mostrarMenu']);
    }

}

class area_atuacao extends Model
{
    //
    protected $primaryKey = 'id';
    public $timestamps = false;
    protected $fillable = ['id','nome','ativo'];

    public function funcaos()
    {
        return $this->belongsToMany(Funcao::class,'fun_area','area_id','fun_id')
            ->as('fun_area')
            ->withPivot(['mostrarMenu']);
    }
}

//controller
    public function store(Request $request)
    {
        //
        if(!empty($request['permissoes']))
        {
            $funcao = null;
            foreach ($request['permissoes'] as $permissoe)
            {
                $idFuncao = (integer)$permissoe["funcao"];

                $funcao = new Funcao();
                $funcao = $funcao->find($idFuncao);
                $funcao->areas()->sync(['area_id'=>$permissoe['area'],'mostrarMenu'=>false]);
            }
        }
    }