You have to assign the certifcate to a specific site.
You can retrieve the binding information of your site using the Get-WebBinding cmdlet and set the SSL Certificate using the AddSslCertificate
function:
$siteName="mywebsite"
$dnsName="www.mywebsite.ru"
# create the ssl certificate
$newCert = New-SelfSignedCertificate -DnsName $dnsName -CertStoreLocation cert:\LocalMachine\My
# get the web binding of the site
$binding = Get-WebBinding -Name $siteName -Protocol "https"
# set the ssl certificate
$binding.AddSslCertificate($newCert.GetCertHashString(), "my")