Now that Amazon Payments is no longer an option for purchases in Cydia, users are forced to use PayPal, at least for the time being. Saurik has noted that he plans on offering an alternative to Cydia, but until that day comes, users are forced to use PayPal.
The problem with PayPal, is that you cannot make a payment via Cydia if you have 2 Factor Authentication (2FA) enabled on your PayPal account. You'll simply receive an error message stating that you need to add your security key to the end of the password in order to login. This, unfortunately, doesn't work, leaving users who haven't set up the initial auth with PayPal unable to purchase Cydia tweaks.
This issue is due to the mobile PayPal interface presented while inside Cydia. If you can bring your authorization outside of Cydia and into mobile safari, you can invoke the desktop interface and login to PayPal that way. Thankfully, a new jailbreak tweak makes this easy.