Here are few suggestions to make your websites more secure:
1. Make sure your root folder (wwwroot or public_html) doesn't have the write permission applied.
2. Check your code and ask the developer to check whether it has any vulnerability.
3. Upgrade your CMS regularly, for example, if you have DNN then upgrade to the newest stable version or apply new patch regularly.
4. Change your FTP password regularly and use the combination of numbers and symbols.