As we have said several times in other threads, companies who are members of the Hays Independence Group are NOT subsiduaries or part of Hays. The "group" is a service Hays sell to independent agents comprising of things like training, access to bed banks, IT and possibly ATOL. The support they get from Hays and the ATOL means there is a good chance of a reasonable holiday but if things went badly wrong you'd have no claim against Hays. There are at least two other groups of this type (Co-op and Global) and dozens of independent agents trade like this.
Wye Travel is based in Guildford in Surrey, the check I can do shows two directors, Mr. Wye (hence the name, nothing to do with Wye Valley) from Guildford and one from across the border in Hampshire who is also the registered owner of the website. Mr Wye is shown as a director of several companies including yourholidays and a timber yard. Wye Travel only seems to have been running for about a year.
If a small company has access to the right reservation systems and is properly bonded (you must make sure you have a proper bonded package not a dynamic package) they can be good. Large companies mean overheads and don't guarantee financial security (ask TC) whilst small companies are cheaper to run but may not have people to help you if you have problems. Take your pick!