I wouldn't complain or make a fuss, I'd just show her delicately that working at home when I need it gets all my stuff done. NB I've worked in jobs where working from home is a 'thing' for around 15 years.
Make sure you do some emails/ask questions/send over stuff to her in the morning, with one email going as soon as you fire up the computer. A few phone calls for clarification or a chat with the office around midday. Then send out the completed work in the late afternoon. If you can, have a 'WFH TO DO list' on the go; and make sure she knows you keep it. Keep it and then if she mentions it again, show her what you have been up to on your last 3 WFH days. Fill up your diary WFH day with slots for different pieces of work. ie 9-10 emails. 10-12:30 Amend and add photos to x report. 12:30-1 lunch 1-3 draft up x. 3-3:30 emails. 3:30-4:30 research x thing. 4:30-5:30 whatever else you do.
If you have broadband, paid for by the company, to enable you to work at home, then make sure you show clear signs that you are using it. Make sure you stack up on your desk all your 'I'm doing this at home on Xday' and mention it regularly in meetings 'I'll do that on Xday, at home where it is quieter. If you have a home office, mention it regularly.
If she mentions it in passing that she doesn't like it then ask 'in what context?' as for you, it means you get more hours in, you catch up with paperwork, you can do long reports with no interruptions, you can get all your emails out of the way first and crack on with X, Y and Z, you always do more hours at home not less ha ha ha every time, yada yada yada, in fact the company get more work out of you on a working from home day and surely that's a good thing? 
I used to manage 17 staff who worked from home, and knew that some didn't do much as I had been their peer and so put measures in place for them to do record their at home, and if they hadn't done it, there were issues. Evidence of working at home are emails and phone calls to the office on regular occasions, plus work actually being finished! If stuff was not being done, monitoring was put in place and actions taken.