Yes, send an apology and revise your conference process accordingly
Firstly, thank-you for your hard work in organising an academic conference. Academics appreciate the hard work done by staff in setting up these events, even if they don't go as planned. The fact that you have worked hard to arrange a conference, arrange invitations for speakers, etc., reflects very well on you, so you needn't worry about being perceived negatively.
Now to the substance of your question. Having low numbers of attendees to talks is an inefficient use of time and academic resources. Consequently, you should consider revising your process in the conference to try to avoid this result in future. It sounds like you have a good number of overall registrants to your conference, and I also note from your comments that you did not hold sessions in parallel. This suggests that you had low engagement per session, which is common for virtual conferences, particularly when registration is free. Nevertheless, it might still indicate that the conference was too long or that there were insufficient opportunities for audience discussion/socialising between sessions. Try to get some information on engagement levels from other virtual conferences and see if there is anything you could be doing better to increase engagement.
The fact that you did not hold sessions in parallel means that each speaker had a full timeslot, without any competition from other speakers, so I think that demonstrates that you were respectful of the value of their time. (Had you held parallel sessions and got this result then that would be much worse!) Nevertheless, it is worth emailing the speakers with an apology, as you propose. Let them know that you are disappointed with the low attendance at the individual talks, that this was a surprise to you given the solid number of registrants, and that you are going to review your process for the conference in future to try to increase engagement. The speakers will probably feel a bit disappointed that they put in a lot of work to prepare a talk and had so few people listen to their talk, and finding out that you share that disappointment (and are looking into ways to fix it) will give them some confidence that this is not the norm. If the speakers do not receive anything from you about the issue then they will assume that this is normal for the events you organise, and that you are comfortable having talks with so few attendees, which will make them less inclined to speak at your conferences in future.
