I work for 1Password, and I wrote exactly about this question when we introduced the feature.
The answer depends on what security properties you actually want from time-based one time passwords (TOTP). The "second factorness" of TOTP one of several security properties it offers, and it may be the least important in many cases. Don't get led astray that this all goes under the term "2FA", as if that is the only security benefit you get from these schemes.
Security benefits of TOTP (contrasted with typical password use)
So I am going to list a few of the security properties you get with TOTP and contrast them with typical password use.
Long term secret isn't transmitted during authentication. With TOTP get a long term secret that is only transmitted (typically the QR code), when you enroll. The long term secret is not transmitted when it is actually used. (This is unlike typical password usage where the password is transmitted over the net, and so depends on other protections, such as TLS). This also means that the long term secret can't be phished (although the numeric codes can be.)
Long term secret is unguessable. The long term secret is generated by the server when you first enroll, and so it is generated up to the service's standards of randomness. Again, this is unlike typical password use with human created passwords.
Long term secret is unique. You will not end up reusing the same TOTP long term secret across various services. Again, this is unlike typical password use, where people reuse passwords.
Oh yeah. And you put the long term secret on "something you have", if for some reason that is important to you.
In most cases where TOTP is deployed, it is done so because of properties #2 (unguessability) and #3 (uniqueness). Indeed, when Dropbox first introduced TOTP on their services, they spelled out their reasons as helping protect users who were reusing passwords.
After the uniqueness and unguessability of the long term secrets, the next most important benefit (for most people) is that the long term secret isn't transmitted. This makes it harder to capture on a compromised network.
Probably the least important of the security properties that TOTP gives us is the second factorness. I'm not saying that there is no benefit to it, but for the cases that most people are using TOTP, it is probably the least important.
Contrasting with using a password manager well.
In the above I listed four security properties of TOTP and contrasted them with typical password use. But now let's consider someone who is using a password manager to its full potential. If you are using a password manager well for some site or service4, you will have randomly generated (and so unguessable) password for that site and you will have unique password for that site. And so the use of TOTP doesn't really add a great deal in terms of those two security properties.
If we look at property #1 (long term secret not transmitted), TOTP still offer some additional security, even if you are using a password manager. However, using a password manager does reduce the chance of getting phished, and so the gain of TOTP, while real, is not as great as it would be for someone not using a password manager.
The only thing left is #4. If the two factorness really is why you value TOTP, then don't keep the long term secret in 1Password. But for most people, the value of TOTP comes from having a strong and unique long term secret that is never transmitted.
Look at the actual security properties
I recommend that you evaluate what you really get out of TOTP (instead of getting caught up in the whole 2FA rhetoric), and then consider the tradeoffs. I'll bet that if things like TOTP where called "Unique Secret Authentication" instead of "Two Factor Authentication" the question would never have come up.