A password manager effectively can't protect against other applications on the same machine. IMO that makes the universality of the clipboard more valuable than the safety of using alternate input methods.
Though since there are plenty of things that block pasting passwords, those alternate options are appreciated.
I agree completely, the clipboard is non-trusted. Yet the fact remains, how can we transmit an arbitrary string from a secure app like a password store, to another app in need of authorization? Lets build constructive conversations.
Ostensibly, yes. Because (as 'StavrosK said), if I don't then we can't even begin to talk about security on that machine yet. We have to start with assumptions somewhere.
If software on your machine is compromised, your machine is compromised (or will be in short order). You need to make reasonable concessions and stick with them in order to get anywhere.
On the other hand it does not work this way in the other direction. Random web pages can manipulate your primary selection and overwrite it with random garbage (this primarily happens with various attempts to make copying stuff from the page more "convenient", pretyy comonly resulting in state when it is simply impossible to copy said thing into say rxvt directly). It is somewhat ironic that chrome's address bar uses some magic to prevent this from happening, while the same magic is not applied to websites.